Compositions and methods for WT1 specific immunotherapy

ABSTRACT

Compositions and methods for the therapy of malignant diseases, such as leukemia and cancer, are disclosed. The compositions comprise a WT1 polypeptide comprising an immunogenic portion of WT1, wherein said WT1 polypeptide comprises the polypeptide of SEQ ID NO:144. Such compositions may be used, for example, for the prevention and treatment of metastatic diseases.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a CIP of U.S. application Ser. No. 09/276,484, filedMar. 21, 1999, which is a CIP of U.S. application Ser. No. 09/164,223,filed Sep. 30, 1998, and are incorporated herein in entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made in part with government support under NIH SBIRPhase I grant number IR43 CA81752-01A1. The Government may have certainrights in this invention.

TECHNICAL FIELD

The present invention relates generally to the immunotherapy ofmalignant diseases such as leukemia and cancers. The invention is morespecifically related to compositions for generating or enhancing animmune response to WT1, and to the use of such compositions forpreventing and/or treating malignant diseases.

BACKGROUND OF THE INVENTION

Cancer and leukemia are significant health problems in the United Statesand throughout the world. Although advances have been made in detectionand treatment of such diseases, no vaccine or other universallysuccessful method for prevention or treatment of cancer and leukemia iscurrently available. Management of the diseases currently relies on acombination of early diagnosis and aggressive treatment, which mayinclude one or more of a variety of treatments such as surgery,radiotherapy, chemotherapy and hormone therapy. The course of treatmentfor a particular cancer is often selected based on a variety ofprognostic parameters, including an analysis of specific tumor markers.However, the use of established markers often leads to a result that isdifficult to interpret, and the high mortality continues to be observedin many cancer patients.

Immunotherapies have the potential to substantially improve cancer andleukemia treatment and survival. Recent data demonstrate that leukemiacan be cured by immunotherapy in the context of bone marrowtransplantation (e.g., donor lymphocyte infusions). Such therapies mayinvolve the generation or enhancement of an immune response to atumor-associated antigen (TAA). However, to date, relatively few TAAsare known and the generation of an immune response against such antigenshas, with rare exceptions, not been shown to be therapeuticallybeneficial.

Accordingly, there is a need in the art for improved methods forleukemia and cancer prevention and therapy. The present inventionfulfills these needs and further provides other related advantages.

SUMMARY OF THE INVENTION

Briefly stated, this invention provides compositions and methods for thediagnosis and therapy of diseases such as leukemia and cancer. In oneaspect, the present invention provides polypeptides comprising animmunogenic portion of a native WT1, or a variant thereof that differsin one or more substitutions, deletions, additions and/or insertionssuch that the ability of the variant to react with antigen-specificantisera and/or T-cell lines or clones is not substantially diminished.Within certain embodiments, the polypeptide comprises no more than 16consecutive amino acid residues of a native WT1 polypeptide. Withinother embodiments, the polypeptide comprises an immunogenic portion ofamino acid residues 1–174 of a native WT1 polypeptide or a variantthereof, wherein the polypeptide comprises no more than 16 consecutiveamino acid residues present within amino acids 175 to 449 of the nativeWT1 polypeptide. The immunogenic portion preferably binds to an MHCclass I and/or class II molecule. Within certain embodiments, thepolypeptide comprises a sequence selected from the group consisting of(a) sequences recited in any one or more of Tables II–XLVI, (b) variantsof the foregoing sequences that differ in one or more substitutions,deletions, additions and/or insertions such that the ability of thevariant to react with antigen-specific antisera and/or T-cell lines orclones is not substantially diminished and (c) mimetics of thepolypeptides recited above, such that the ability of the mimetic toreact with antigen-specific antisera and/or T cell lines or clones isnot substantially diminished.

Within other embodiments, the polypeptide comprises a sequence selectedfrom the group consisting of (a) ALLPAVPSL (SEQ ID NO:34), GATLKGVAA(SEQ ID NO:88), CMTWNQMNL (SEQ ID NOs: 49 and 258), SCLESQPTI (SEQ IDNOs: 199 and 296), SCLESQPAI (SEQ ID NO:198), NLYQMTSQL (SEQ ID NOs: 147and 284), ALLPAVSSL (SEQ ID NOs: 35 and 255), RMFPNAPYL (SEQ ID NOs: 185and 293), (b) variants of the foregoing sequences that differ in one ormore substitutions, deletions, additions and/or insertions such that theability of the variant to react with antigen-specific antisera and/orT-cell lines or clones is not substantially diminished and (c) mimeticsof the polypeptides recited above, such that the ability of the mimeticto react with antigen-specific antisera and/or T cell lines or clones isnot substantially diminished. Mimetics may comprises amino acids incombination with one or more amino acid mimetics or may be entirelynonpeptide mimetics.

Within further aspects, the present invention provides polypeptidescomprising a variant of an immunogenic portion of a WT1 protein, whereinthe variant differs from the immunogenic portion due to substitutions atbetween 1 and 3 amino acid positions within the immunogenic portion suchthat the ability of the variant to react with antigen-specific antiseraand/or T-cell lines or clones is enhanced relative to a native WT1protein.

The present invention further provides WT1 polynucleotides that encode aWT1 polypeptide as described above.

Within other aspects, the present invention provides pharmaceuticalcompositions and vaccines. Pharmaceutical compositions may comprise apolypeptide or mimetic as described above and/or one or more of (i) aWT1 polynucleotide; (ii) an antibody or antigen-binding fragment thereofthat specifically binds to a WT1 polypeptide; (iii) a T cell thatspecifically reacts with a WT1 polypeptide or (iv) an antigen-presentingcell that expresses a WT1 polypeptide, in combination with apharmaceutically acceptable carrier or excipient. Vaccines comprise apolypeptide as described above and/or one or more of (i) a WT1polynucleotide, (ii) an antigen-presenting cell that expresses a WT1polypeptide or (iii) an anti-idiotypic antibody, and a non-specificimmune response enhancer. Within certain embodiments, less than 23consecutive amino acid residues, preferably less than 17 amino acidresidues, of a native WT1 polypeptide are present within a WT1polypeptide employed within such pharmaceutical compositions andvaccines. The immune response enhancer may be an adjuvant. Preferably,an immune response enhancer enhances a T cell response.

The present invention further provides methods for enhancing or inducingan immune response in a patient, comprising administering to a patient apharmaceutical composition or vaccine as described above. In certainembodiments, the patient is a human.

The present invention further provides methods for inhibiting thedevelopment of a malignant disease in a patient, comprisingadministering to a patient a pharmaceutical composition or vaccine asdescribed above. Malignant diseases include, but are not limited toleukemias (e.g., acute myeloid, acute lymphocytic and chronic myeloid)and cancers (e.g., breast, lung, thyroid or gastrointestinal cancer or amelanoma). The patient may, but need not, be afflicted with themalignant disease, and the administration of the pharmaceuticalcomposition or vaccine may inhibit the onset of such a disease, or mayinhibit progression and/or metastasis of an existing disease.

The present invention further provides, within other aspects, methodsfor removing cells expressing WT1 from bone marrow and/or peripheralblood or fractions thereof, comprising contacting bone marrow,peripheral blood or a fraction of bone marrow or peripheral blood with Tcells that specifically react with a WT1 polypeptide, wherein the stepof contacting is performed under conditions and for a time sufficient topermit the removal of WT1 positive cells to less than 10%, preferablyless than 5% and more preferably less than 1%, of the number of myeloidor lymphatic cells in the bone marrow, peripheral blood or fraction.Bone marrow, peripheral blood and fractions may be obtained from apatient afflicted with a disease associated with WT1 expression, or maybe obtained from a human or non-human mammal not afflicted with such adisease.

Within related aspects, the present invention provides methods forinhibiting the development of a malignant disease in a patient,comprising administering to a patient bone marrow, peripheral blood or afraction of bone marrow or peripheral blood prepared as described above.Such bone marrow, peripheral blood or fractions may be autologous, ormay be derived from a related or unrelated human or non-human animal(e.g., syngeneic or allogeneic).

In other aspects, the present invention provides methods for stimulating(or priming) and/or expanding T cells, comprising contacting T cellswith a WT1 polypeptide under conditions and for a time sufficient topermit the stimulation and/or expansion of T cells. Such T cells may beautologous, allogeneic, syngeneic or unrelated WT1-specific T cells, andmay be stimulated in vitro or in vivo. Expanded T cells may, withincertain embodiments, be present within bone marrow, peripheral blood ora fraction of bone marrow or peripheral blood, and may (but need not) beclonal. Within certain embodiments, T cells may be present in a mammalduring stimulation and/or expansion. WT1-specific T cells may be used,for example, within donor lymphocyte infusions.

Within related aspects, methods are provided for inhibiting thedevelopment of a malignant disease in a patient, comprisingadministering to a patient T cells prepared as described above. Such Tcells may, within certain embodiments, be autologous, syngeneic orallogeneic.

The present invention further provides, within other aspects, methodsfor monitoring the effectiveness of an immunization or therapy for amalignant disease associated with WT1 expression in a patient. Suchmethods are based on monitoring antibody, CD4+ T cell and/or CD8+ T cellresponses in the patient. Within certain such aspects, a method maycomprise the steps of: (a) incubating a first biological sample with oneor more of: (i) a WT1 polypeptide; (ii) a polynucleotide encoding a WT1polypeptide; or (iii) an antigen presenting cell that expresses a WT1polypeptide, wherein the first biological sample is obtained from apatient prior to a therapy or immunization, and wherein the incubationis performed under conditions and for a time sufficient to allowimmunocomplexes to form; (b) detecting immunocomplexes formed betweenthe WT1 polypeptide and antibodies in the biological sample thatspecifically bind to the WT1 polypeptide; (c) repeating steps (a) and(b) using a second biological sample obtained from the same patientfollowing therapy or immunization; and (d) comparing the number ofimmunocomplexes detected in the first and second biological samples, andtherefrom monitoring the effectiveness of the therapy or immunization inthe patient.

Within certain embodiments of the above methods, the step of detectingcomprises (a) incubating the immunocomplexes with a detection reagentthat is capable of binding to the immunocomplexes, wherein the detectionreagent comprises a reporter group, (b) removing unbound detectionreagent, and (c) detecting the presence or absence of the reportergroup. The detection reagent may comprise, for example, a secondantibody, or antigen-binding fragment thereof, capable of binding to theantibodies that specifically bind to the WT1 polypeptide or a moleculesuch as Protein A. Within other embodiments, a reporter group is boundto the WT1 polypeptide, and the step of detecting comprises removingunbound WT1 polypeptide and subsequently detecting the presence orabsence of the reporter group.

Within further aspects, methods for monitoring the effectiveness of animmunization or therapy for a malignant disease associated with WT1expression in a patient may comprise the steps of: (a) incubating afirst biological sample with one or more of: (i) a WT1 polypeptide; (ii)a polynucleotide encoding a WT1 polypeptide; or (iii) an antigenpresenting cell that expresses a WT1 polypeptide, wherein the biologicalsample comprises CD4+ and/or CD8+ T cells and is obtained from a patientprior to a therapy or immunization, and wherein the incubation isperformed under conditions and for a time sufficient to allow specificactivation, proliferation and/or lysis of T cells; (b) detecting anamount of activation, proliferation and/or lysis of the T cells; (c)repeating steps (a) and (b) using a second biological sample comprisingCD4+ and/or CD8+ T cells, wherein the second biological sample isobtained from the same patient following therapy or immunization; and(d) comparing the amount of activation, proliferation and/or lysis of Tcells in the first and second biological samples, and therefrommonitoring the effectiveness of the therapy or immunization in thepatient.

The present invention further provides methods for inhibiting thedevelopment of a malignant disease associated with WT1 expression in apatient, comprising the steps of: (a) incubating CD4⁺ and/or CD8+ Tcells isolated from a patient with one or more of: (i) a WT1polypeptide; (ii) a polynucleotide encoding a WT1 polypeptide; or (iii)an antigen presenting cell that expresses a WT1 polypeptide, such thatthe T cells proliferate; and (b) administering to the patient aneffective amount of the proliferated T cells, and therefrom inhibitingthe development of a malignant disease in the patient. Within certainembodiments, the step of incubating the T cells may be repeated one ormore times.

Within other aspects, the present invention provides methods forinhibiting the development of a malignant disease associated with WT1expression in a patient, comprising the steps of: (a) incubating CD4⁺and/or CD8+ T cells isolated from a patient with one or more of: (i) aWT1 polypeptide; (ii) a polynucleotide encoding a WT1 polypeptide; or(iii) an antigen presenting cell that expresses a WT1 polypeptide, suchthat the T cells proliferate; (b) cloning one or more cells thatproliferated; and (c) administering to the patient an effective amountof the cloned T cells.

Within other aspects, methods are provided for determining the presenceor absence of a malignant disease associated with WT1 expression in apatient, comprising the steps of: (a) incubating CD4⁺ and/or CD8+ Tcells isolated from a patient with one or more of: (i) a WT1polypeptide; (ii) a polynucleotide encoding a WT1 polypeptide; or (iii)an antigen presenting cell that expresses a WT1 polypeptide; and (b)detecting the presence or absence of specific activation of the T cells,therefrom determining the presence or absence of a malignant diseaseassociated with WT1 expression. Within certain embodiments, the step ofdetecting comprises detecting the presence or absence of proliferationof the T cells.

Within further aspects, the present invention provides methods fordetermining the presence or absence of a malignant disease associatedwith WT1 expression in a patient, comprising the steps of: (a)incubating a biological sample obtained from a patient with one or moreof: (i) a WT1 polypeptide; (ii) a polynucleotide encoding a WT1polypeptide; or (iii) an antigen presenting cell that expresses a WT1polypeptide, wherein the incubation is performed under conditions andfor a time sufficient to allow immunocomplexes to form; and (b)detecting immunocomplexes formed between the WT1 polypeptide andantibodies in the biological sample that specifically bind to the WT1polypeptide; and therefrom determining the presence or absence of amalignant disease associated with WT1 expression.

These and other aspects of the present invention will become apparentupon reference to the following detailed description and attacheddrawings. All references disclosed herein are hereby incorporated byreference in their entirety as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a comparison of the mouse (MO) and human (HU) WT1 proteinsequences (SEQ ID NOS: 320 and 319 respectively).

FIG. 2 is a Western blot illustrating the detection of WT1 specificantibodies in patients with hematological malignancy (AML). Lane 1 showsmolecular weight markers; lane 2 shows a positive control (WT1 positivehuman leukemia cell line immunoprecipitated with a WT1 specificantibody); lane 3 shows a negative control (WT1 positive cell lineimmunoprecipitated with mouse sera); and lane 4 shows a WT1 positivecell line immunoprecipitated with sera of a patient with AML. For lanes2–4, the immunoprecipitate was separated by gel electrophoresis andprobed with a WT1 specific antibody.

FIG. 3 is a Western blot illustrating the detection of a WT1 specificantibody response in B6 mice immunized with TRAMP-C, a WT1 positivetumor cell line. Lanes 1, 3 and 5 show molecular weight markers, andlanes 2, 4 and 6 show a WT1 specific positive control (N180, Santa CruzBiotechnology, polypeptide spanning 180 amino acids of the N-terminalregion of the WT1 protein, migrating on the Western blot at 52 kD). Theprimary antibody used was WT180 in lane 2, sera of non-immunized B6 micein lane 4 and sera of the immunized B6 mice in lane 6.

FIG. 4 is a Western blot illustrating the detection of WT1 specificantibodies in mice immunized with representative WT1 peptides. Lanes 1,3 and 5 show molecular weight markers and lanes 2, 4 and 6 show a WT1specific positive control (N180, Santa Cruz Biotechnology, polypeptidespanning 180 amino acids of the N-terminal region of the WT1 protein,migrating on the Western blot at 52 kD). The primary antibody used wasWT180 in lane 2, sera of non-immunized B6 mice in lane 4 and sera of theimmunized B6 mice in lane 6.

FIGS. 5A to 5C are graphs illustrating the stimulation of proliferativeT cell responses in mice immunized with representative WT1 peptides.Thymidine incorporation assays were performed using one T cell line andtwo different clones, as indicated, and results were expressed as cpm.Controls indicated on the x axis were no antigen (No Ag) and B6/media;antigens used were p6–22 human (p1), p117–139 (p2) or p244–262 human(p3).

FIGS. 6A and 6B are histograms illustrating the stimulation ofproliferative T cell responses in mice immunized with representative WT1peptides. Three weeks after the third immunization, spleen cells of micethat had been inoculated with Vaccine A or Vaccine B were cultured withmedium alone (medium) or spleen cells and medium (B6/no antigen), B6spleen cells pulsed with the peptides p6–22 (p6), p117–139 (p117),p244–262 (p244) (Vaccine A; FIG. 6A) or p287–301 (p287), p299–313(p299), p421–435 (p421) (Vaccine B; FIG. 6B) and spleen cells pulsedwith an irrelevant control peptide (irrelevant peptide) at 25 ug/ml andwere assayed after 96 hr for proliferation by (3H) thymidineincorporation. Bars represent the stimulation index (SI), which iscalculated as the mean of the experimental wells divided by the mean ofthe control (B6 spleen cells with no antigen).

FIGS. 7A–7D are histograms illustrating the generation of proliferativeT-cell lines and clones specific for p117–139 and p6–22. Following invivo immunization, the initial three in vitro stimulations (IVS) werecarried out using all three peptides of Vaccine A or B, respectively.Subsequent IVS were carried out as single peptide stimulations usingonly the two relevant peptides p117–139 and p6–22. Clones were derivedfrom both the p6–22 and p117–139 specific T cell lines, as indicated. Tcells were cultured with medium alone (medium) or spleen cells andmedium (B6/no antigen), B6 spleen cells pulsed with the peptides p6–22(p6), p117–139 (p117) or an irrelevant control peptide (irrelevantpeptide) at 25 ug/ml and were assayed after 96 hr for proliferation by(3H) thymidine incorporation. Bars represent the stimulation index (SI),which is calculated as the mean of the experimental wells divided by themean of the control (B6 spleen cells with no antigen).

FIGS. 8A and 8B present the results of TSITES Analysis of human WT1 (SEQID NO:319) for peptides that have the potential to elicit Th responses.Regions indicated by “A” are AMPHI midpoints of blocks, “R” indicatesresidues matching the Rothbard/Taylor motif, “D” indicates residuesmatching the IAd motif, and ‘d’ indicates residues matching the IEdmotif.

FIGS. 9A and 9B are graphs illustrating the elicitation of WT1peptide-specific CTL in mice immunized with WT1 peptides. FIG. 9Aillustrates the lysis of target cells by allogeneic cell lines and FIG.9B shows the lysis of peptide coated cell lines. In each case, the %lysis (as determined by standard chromium release assays) is shown atthree indicated effector:target ratios. Results are provided forlymphoma cells (LSTRA and E10), as well as E10+p235–243 (E10+P235). E10cells are also referred to herein as EL-4 cells.

FIGS. 10A–10D are graphs illustrating the elicitation of WT1 specificCTL, which kill WT1 positive tumor cell lines but do not kill WT1negative cell lines, following vaccination of B6 mice with WT1 peptideP117. FIG. 10A illustrates that T-cells of non-immunized B6 mice do notkill WT1 positive tumor cell lines. FIG. 10B illustrates the lysis ofthe target cells by allogeneic cell lines. FIGS. 10C and 10D demonstratethe lysis of WT1 positive tumor cell lines, as compared to WT1 negativecell lines in two different experiments. In addition, FIGS. 10C and 10Dshow the lysis of peptide-coated cell lines (WT1 negative cell line E10coated with the relevant WT1 peptide P117) In each case, the % lysis (asdetermined by standard chromium release assays) is shown at threeindicated effector:target ratios. Results are provided for lymphomacells (E10), prostate cancer cells (TRAMP-C), a transformed fibroblastcell line (BLK-SV40), as well as E10+p117.

FIGS. 11A and 11B are histograms illustrating the ability ofrepresentative peptide P117–139 specific CTL to lyse WT1 positive tumorcells. Three weeks after the third immunization, spleen cells of micethat had been inoculated with the peptides p235–243 or p117–139 werestimulated in vitro with the relevant peptide and tested for ability tolyse targets incubated with WT1 peptides as well as WT1 positive andnegative tumor cells. The bars represent the mean % specific lysis inchromium release assays performed in triplicate with an E:T ratio of25:1. FIG. 1A shows the cytotoxic activity of the p235–243 specific Tcell line against the WT1 negative cell line EL-4 (EL-4, WT1 negative);EL-4 pulsed with the relevant (used for immunization as well as forrestimulation) peptide p235–243 (EL-4+p235); EL-4 pulsed with theirrelevant peptides p117–139 (EL-4+p117), p126–134 (EL-4+p126) orp130–138 (EL-4+p130) and the WT1 positive tumor cells BLK-SV40(BLK-SV40, WT1 positive) and TRAMP-C (TRAMP-C, WT1 positive), asindicated. FIG. 11B shows cytotoxic activity of the p117–139 specific Tcell line against EL-4; EL-4 pulsed with the relevant peptide P117–139(EL-4+p117) and EL-4 pulsed with the irrelevant peptides p123–131(EL-4+p123), or p128–136 (EL-4+p128); BLK-SV40 and TRAMP-C, asindicated.

FIGS. 12A and 12B are histograms illustrating the specificity of lysisof WT1 positive tumor cells, as demonstrated by cold target inhibition.The bars represent the mean % specific lysis in chromium release assaysperformed in triplicate with an E:T ratio of 25:1. FIG. 12A shows thecytotoxic activity of the p117–139 specific T cell line against the WT1negative cell line EL-4 (EL-4, WT1 negative); the WT1 positive tumorcell line TRAMP-C (TRAMP-C, WT1 positive); TRAMP-C cells incubated witha ten-fold excess (compared to the hot target) of EL-4 cells pulsed withthe relevant peptide p117–139 (TRAMP-C+p117 cold target) without ⁵¹Crlabeling and TRAMP-C cells incubated with EL-4 pulsed with an irrelevantpeptide without ⁵¹Cr labeling (TRAMP-C+irrelevant cold target), asindicated. FIG. 12B shows the cytotoxic activity of the p117–139specific T cell line against the WT1 negative cell line EL-4 (EL-4, WT1negative); the WT1 positive tumor cell line BLK-SV40 (BLK-SV40, WT1positive); BLK-SV40 cells incubated with the relevant cold target(BLK-SV40+p117 cold target) and BLK-SV40 cells incubated with theirrelevant cold target (BLK-SV40+irrelevant cold target), as indicated.

FIGS. 13A–13C are histograms depicting an evaluation of the 9mer CTLepitope within p117–139. The p117–139 tumor specific CTL line was testedagainst peptides within aa117–139 containing or lacking an appropriateH-2^(b) class I binding motif and following restimulation with p126–134or p130–138. The bars represent the mean % specific lysis in chromiumrelease assays performed in triplicate with an E:T ratio of 25:1. FIG.13A shows the cytotoxic activity of the p117–139 specific T cell lineagainst the WT1 negative cell line EL-4 (EL-4, WT1 negative) and EL-4cells pulsed with the peptides p117–139 (EL-4+p117), p119–127(EL-4+p119), p120–128 (EL-4+p120), p123–131 (EL-4+p123), p126–134(EL-4+p126), p128–136 (EL-4+p128), and p130–138 (EL-4+p130). FIG. 13Bshows the cytotoxic activity of the CTL line after restimulation withp126–134 against the WT1 negative cell line EL-4, EL-4 cells pulsed withp117–139 (EL-4+p117), p126–134 (EL-4+p126) and the WT1 positive tumorcell line TRAMP-C. FIG. 13C shows the cytotoxic activity of the CTL lineafter restimulation with p130–138 against EL-4, EL-4 cells pulsed withp117–139 (EL-4+p117), p130–138 (EL-4+p130) and the WT1 positive tumorcell line TRAMP-C.

FIG. 14 depicts serum antibody reactivity to WT1 in 63 patients withAML. Reactivity of serum antibody to WT1/N-terminus protein wasevaluated by ELISA in patients with AML. The first and second lanesrepresent the positive and negative controls, respectively. The firstand second lanes represent the ositive and negative controls,respectively. Commercially obtained WT1 specific antibody WT180 was usedfor the positive control. The next 63 lanes represent results using serafrom each individual patient. The OD values depicted were from ELISAusing a 1:500 serum dilution. The figure includes cumulative data from 3separate experiments.

FIG. 15 depicts serum antibody reactivity to WT1 proteins and controlproteins in 2 patients with AML. Reactivity of serum antibody toWT1/full-length, WT1N-terminus, TRX and Ra12 proteins was evaluated byELISA in 2 patients with AML. The OD values depicted were from ELISAusing a 1:500 serum dilution. AML-1 and AML-2 denote serum from 2 of theindividual patients in FIG. 1 with demonstrated antibody reactivity toWT1/full-length. The WT1 full-length protein was expressed as a fusionprotein with Ra12. The WT1/N-terminus protein was expressed as a fusionprotein with TRX. The control Ra12 and TRX proteins were purified in asimilar manner. The results confirm that the serum antibody reactivityagainst the WT1 fusion proteins is directed against the WT1 portions ofthe protein.

FIG. 16 depicts serum antibody reactivity to WT1 in 81 patients withCML. Reactivity of serum antibody to WT1/full-length protein wasevaluated by ELISA in patients with AML. The first and second lanesrepresent the positive and negative controls, respectively. Commerciallyobtained WT1 specific antibody WT180 was used for the positive control.The next 81 lanes represent results using sera from each individualpatient. The OD values depicted were from ELISA using a 1:500 serumdilution. The figure includes cumulative data from 3 separateexperiments.

FIG. 17 depicts serum antibody reactivity to WT1 proteins and controlproteins in 2 patients with CML. Reactivity of serum antibody toWT1/full-length, WT1/N-terminus, TRX and Ra12 proteins was evaluated byELISA in 2 patients with CML. The OD values depicted were from ELISAusing a 1:500 serum dilution. CML-1 and CML-2 denote serum from 2 of theindividual patients in FIG. 3 with demonstrated antibody reactivity toWT1/full-length. The WT1/full-length protein was expressed as a fusionprotein with Ra12. The WT1/N-terminus protein was expressed as a fusionprotein with TRX. The control Ra12 and TRX proteins were purified in asimilar manner. The results confirm that the serum antibody reactivityagainst the WT1 fusion proteins is directed against the WT1 portions ofthe protein.

FIG. 18 provides the characteristics of the recombinant WT1 proteinsused for serological analysis.

FIG. 19 provides the specific serum antibodies in patients with AML andCML.

DETAILED DESCRIPTION OF THE INVENTION

As noted above, the present invention is generally directed tocompositions and methods for the immunotherapy and diagnosis ofmalignant diseases. The compositions described herein may include WT1polypeptides, WT1 polynucleotides, antigen-presenting cells (APC, e.g.,dendritic cells) that express a WT1 polypeptide, agents such asantibodies that bind to a WT1 polypeptide and/or immune system cells(e.g., T cells) specific for WT1. WT1 Polypeptides of the presentinvention generally comprise at least a portion of a Wilms Tumor geneproduct (WT1) or a variant thereof. Nucleic acid sequences of thesubject invention generally comprise a DNA or RNA sequence that encodesall or a portion of such a polypeptide, or that is complementary to sucha sequence. Antibodies are generally immune system proteins, orantigen-binding fragments thereof, that are capable of binding to aportion of a WT1 polypeptide. T cells that may be employed within suchcompositions are generally T cells (e.g., CD4⁺ and/or CD8⁺) that arespecific for a WT1 polypeptide. Certain methods described herein furtheremploy antigen-presenting cells that express a WT1 polypeptide asprovided herein.

The present invention is based on the discovery that an immune responseraised against a Wilms Tumor (WT) gene product (e.g., WT1) can provideprophylactic and/or therapeutic benefit for patients afflicted withmalignant diseases characterized by increased WT1 gene expression. Suchdiseases include, but are not limited to, leukemias (e.g., acute myeloidleukemia (AML), chronic myeloid leukemia (CML), acute lymphocyticleukemia (ALL) and childhood ALL), as well as many cancers such as lung,breast, thyroid and gastrointestinal cancers and melanomas. The WT1 genewas originally identified and isolated on the basis of a cytogeneticdeletion at chromosome 11p13 in patients with Wilms' tumor (see Call etal., U.S. Pat. No. 5,350,840). The gene consists of 10 exons and encodesa zinc finger transcription factor, and sequences of mouse and human WT1proteins are provided in FIG. 1 and SEQ ID NOs: 319 and 320.

WT1 Polypeptides

Within the context of the present invention, a WT1 polypeptide is apolypeptide that comprises at least an immunogenic portion of a nativeWT1 (i.e., a WT1 protein expressed by an organism that is notgenetically modified), or a variant thereof, as described herein. A WT1polypeptide may be of any length, provided that it comprises at least animmunogenic portion of a native protein or a variant thereof. In otherwords, a WT1 polypeptide may be an oligopeptide (i.e., consisting of arelatively small number of amino acid residues, such as 8–10 residues,joined by peptide bonds), a full length WT1 protein (e.g., presentwithin a human or non-human animal, such as a mouse) or a polypeptide ofintermediate size. Within certain embodiments, the use of WT1polypeptides that contain a small number of consecutive amino acidresidues of a native WT1 polypeptide is preferred. Such polypeptides arepreferred for certain uses in which the generation of a T cell responseis desired. For example, such a WT1 polypeptide may contain less than23, preferably no more than 18, and more preferably no more than 15consecutive amino acid residues, of a native WT1 polypeptide.Polypeptides comprising nine consecutive amino acid residues of a nativeWT1 polypeptide are generally suitable for such purposes. Additionalsequences derived from the native protein and/or heterologous sequencesmay be present within any WT1 polypeptide, and such sequences may (butneed not) possess further immunogenic or antigenic properties.Polypeptides as provided herein may further be associated (covalently ornoncovalently) with other polypeptide or non-polypeptide compounds.

An “immunogenic portion,” as used herein is a portion of a polypeptidethat is recognized (i.e., specifically bound) by a B-cell and/or T-cellsurface antigen receptor. Certain preferred immunogenic portions bind toan MHC class I or class II molecule. As used herein, an immunogenicportion is said to “bind to” an MHC class I or class II molecule if suchbinding is detectable using any assay known in the art. For example, theability of a polypeptide to bind to MHC class I may be evaluatedindirectly by monitoring the ability to promote incorporation of ¹²⁵Ilabeled β2-microglobulin (β2m) into MHC class I/β2 m/peptideheterotrimeric complexes (see Parker et al., J. Immunol. 152:163, 1994).Alternatively, functional peptide competition assays that are known inthe art may be employed. Certain immunogenic portions have one or moreof the sequences recited within one or more of Tables II–XIV.Representative immunogenic portions include, but are not limited to,RDLNALLPAVPSLGGGG (human WT1 residues 6–22; SEQ ID NO: 1),PSQASSGQARMFPNAPYLPSCLE (human and mouse WT1 residues 117–139; SEQ IDNOs: 2 and 3 respectively), GATLKGVAAGSSSSVKWTE (human WT1 residues244–262; SEQ ID NO:4), GATLKGVAA (human WT1 residues 244–252; SEQ IDNO:88), CMTWNQMNL (human and mouse WT1 residues 235–243; SEQ ID NOs: 49and 258 respectively), SCLESQPTI (mouse WT1 residues 136–144; SEQ IDNO:296), SCLESQPAI (human WT1 residues 136–144; SEQ ID NO:198),NLYQMTSQL (human and mouse WT1 residues 225–233; SEQ ID NOs: 147 and 284respectively); ALLPAVSSL (mouse WT1 residues 10–18; SEQ ID NO:255); orRMFPNAPYL (human and mouse WT1 residues 126–134; SEQ ID NOs: 185 and 293respectively). Further immunogenic portions are provided herein, andothers may generally be identified using well known techniques, such asthose summarized in Paul, Fundamental Immunology, 3rd ed., 243–247(Raven Press, 1993) and references cited therein. Representativetechniques for identifying immunogenic portions include screeningpolypeptides for the ability to react with antigen-specific antiseraand/or T-cell lines or clones. An immunogenic portion of a native WT1polypeptide is a portion that reacts with such antisera and/or T-cellsat a level that is not substantially less than the reactivity of thefull length WT1 (e.g., in an ELISA and/or T-cell reactivity assay). Inother words, an immunogenic portion may react within such assays at alevel that is similar to or greater than the reactivity of the fulllength polypeptide. Such screens may generally be performed usingmethods well known to those of ordinary skill in the art, such as thosedescribed in Harlow and Lane, Antibodies: A Laboratory Manual, ColdSpring Harbor Laboratory, 1988.

Alternatively, immunogenic portions may be identified using computeranalysis, such as the Tsites program (see Rothbard and Taylor, EMBO J.7:93–100, 1988; Deavin et al., Mol. Immunol. 33:145–155, 1996), whichsearches for peptide motifs that have the potential to elicit Thresponses. CTL peptides with motifs appropriate for binding to murineand human class I or class II MHC may be identified according to BIMAS(Parker et al., J. Immunol. 152:163, 1994) and other HLA peptide bindingprediction analyses. To confirm immunogenicity, a peptide may be testedusing an HLA A2 transgenic mouse model and/or an in vitro stimulationassay using dendritic cells, fibroblasts or peripheral blood cells.

As noted above, a composition may comprise a variant of a native WT1protein. A polypeptide “variant,” as used herein, is a polypeptide thatdiffers from a native polypeptide in one or more substitutions,deletions, additions and/or insertions, such that the immunogenicity ofthe polypeptide is retained (i.e., the ability of the variant to reactwith antigen-specific antisera and/or T-cell lines or clones is notsubstantially diminished relative to the native polypeptide). In otherwords, the ability of a variant to react with antigen-specific antiseraand/or T-cell lines or clones may be enhanced or unchanged, relative tothe native polypeptide, or may be diminished by less than 50%, andpreferably less than 20%, relative to the native polypeptide. Suchvariants may generally be identified by modifying one of the abovepolypeptide sequences and evaluating the reactivity of the modifiedpolypeptide with antisera and/or T-cells as described herein. It hasbeen found, within the context of the present invention, that arelatively small number of substitutions (e.g., 1 to 3) within animmunogenic portion of a WT1 polypeptide may serve to enhance theability of the polypeptide to elicit an immune response. Suitablesubstitutions may generally be identified by using computer programs, asdescribed above, and the effect confirmed based on the reactivity of themodified polypeptide with antisera and/or T-cells as described herein.Accordingly, within certain preferred embodiments, a WT1 polypeptidecomprises a variant in which 1 to 3 amino acid resides within animmunogenic portion are substituted such that the ability to react withantigen-specific antisera and/or T-cell lines or clones is statisticallygreater than that for the unmodified polypeptide. Such substitutions arepreferably located within an MHC binding site of the polypeptide, whichmay be identified as described above. Preferred substitutions allowincreased binding to MHC class I or class II molecules.

Certain variants contain conservative substitutions. A “conservativesubstitution” is one in which an amino acid is substituted for anotheramino acid that has similar properties, such that one skilled in the artof peptide chemistry would expect the secondary structure andhydropathic nature of the polypeptide to be substantially unchanged.Amino acid substitutions may generally be made on the basis ofsimilarity in polarity, charge, solubility, hydrophobicity,hydrophilicity and/or the amphipathic nature of the residues. Forexample, negatively charged amino acids include aspartic acid andglutamic acid; positively charged amino acids include lysine andarginine; and amino acids with uncharged polar head groups havingsimilar hydrophilicity values include leucine, isoleucine and valine;glycine and alanine; asparagine and glutamine; and serine, threonine,phenylalanine and tyrosine. Other groups of amino acids that mayrepresent conservative changes include: (1) ala, pro, gly, glu, asp,gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala,phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also,or alternatively, contain nonconservative changes. Variants may also (oralternatively) be modified by, for example, the deletion or addition ofamino acids that have minimal influence on the immunogenicity, secondarystructure and hydropathic nature of the polypeptide.

In a preferred embodiment, a variant polypeptide of the WT1 N-terminus(amino acids 1–249) is constructed, wherein the variant polypeptide iscapable of binding to an antibody that recognizes full-length WT1 and/orWT1 N-terminus polypeptide. A non-limiting example of an antibody isanti WT-1 antibody WT180 (Santa Cruz Biotechnology, Inc., Santa Cruz,Calif.).

As noted above, WT1 polypeptides may be conjugated to a signal (orleader) sequence at the N-terminal end of the protein whichco-translationally or post-translationally directs transfer of theprotein. A polypeptide may also, or alternatively, be conjugated to alinker or other sequence for ease of synthesis, purification oridentification of the polypeptide (e.g., poly-His), or to enhancebinding of the polypeptide to a solid support. For example, apolypeptide may be conjugated to an immunoglobulin Fc region.

WT1 polypeptides may be prepared using any of a variety of well knowntechniques. Recombinant polypeptides encoded by a WT1 polynucleotide asdescribed herein may be readily prepared from the polynucleotide. Ingeneral, any of a variety of expression vectors known to those ofordinary skill in the art may be employed to express recombinant WT1polypeptides. Expression may be achieved in any appropriate host cellthat has been transformed or transfected with an expression vectorcontaining a DNA molecule that encodes a recombinant polypeptide.Suitable host cells include prokaryotes, yeast and higher eukaryoticcells. Preferably, the host cells employed are E. Coli, yeast or amammalian cell line such as COS or CHO. Supernatants from suitablehost/vector systems which secrete recombinant protein or polypeptideinto culture media may be first concentrated using a commerciallyavailable filter. The concentrate may then be applied to a suitablepurification matrix such as an affinity matrix or an ion exchange resin.Finally, one or more reverse phase HPLC steps can be employed to furtherpurify a recombinant polypeptide. Such techniques may be used to preparenative polypeptides or variants thereof. For example, polynucleotidesthat encode a variant of a native polypeptide may generally be preparedusing standard mutagenesis techniques, such as oligonucleotide-directedsite-specific mutagenesis, and sections of the DNA sequence may beremoved to permit preparation of truncated polypeptides.

Certain portions and other variants may also be generated by syntheticmeans, using techniques well known to those of ordinary skill in theart. For example, polypeptides having fewer than about 500 amino acids,preferably fewer than about 100 amino acids, and more preferably fewerthan about 50 amino acids, may be synthesized. Polypeptides may besynthesized using any of the commercially available solid-phasetechniques, such as the Merrifield solid-phase synthesis method, whereamino acids are sequentially added to a growing amino acid chain. SeeMerrifield, J. Am. Chem. Soc. 85:2149–2146, 1963. Equipment forautomated synthesis of polypeptides is commercially available fromsuppliers such as Applied BioSystems, Inc. (Foster City, Calif.), andmay be operated according to the manufacturer's instructions.

In general, polypeptides and polynucleotides as described herein areisolated. An “isolated” polypeptide or polynucleotide is one that isremoved from its original environment. For example, anaturally-occurring protein is isolated if it is separated from some orall of the coexisting materials in the natural system. Preferably, suchpolypeptides are at least about 90% pure, more preferably at least about95% pure and most preferably at least about 99% pure. A polynucleotideis considered to be isolated if, for example, it is cloned into a vectorthat is not a part of the natural environment.

Within further aspects, the present invention provides mimetics of WT1polypeptides. Such mimetics may comprise amino acids linked to one ormore amino acid mimetics (i.e., one or more amino acids within the WT1protein may be replaced by an amino acid mimetic) or may be entirelynonpeptide mimetics. An amino acid mimetic is a compound that isconformationally similar to an amino acid such that it can besubstituted for an amino acid within a WT1 polypeptide withoutsubstantially diminishing the ability to react with antigen-specificantisera and/or T cell lines or clones. A nonpeptide mimetic is acompound that does not contain amino acids, and that has an overallconformation that is similar to a WT1 polypeptide such that the abilityof the mimetic to react with WT1-specific antisera and/or T cell linesor clones is not substantially diminished relative to the ability of aWT1 polypeptide. Such mimetics may be designed based on standardtechniques (e.g., nuclear magnetic resonance and computationaltechniques) that evaluate the three dimensional structure of a peptidesequence. Mimetics may be designed where one or more of the side chainfunctionalities of the WT1 polypeptide are replaced by groups that donot necessarily have the same size or volume, but have similar chemicaland/or physical properties which produce similar biological responses.It should be understood that, within embodiments described herein, amimetic may be substituted for a WT1 polypeptide.

Within other illustrative embodiments, a polypeptide may be a fusionpolypeptide that comprises multiple polypeptides as described herein, orthat comprises at least one polypeptide as described herein and anunrelated sequence, such as a known tumor protein. A fusion partner may,for example, assist in providing T helper epitopes (an immunologicalfusion partner), preferably T helper epitopes recognized by humans, ormay assist in expressing the protein (an expression enhancer) at higheryields than the native recombinant protein. Certain preferred fusionpartners are both immunological and expression enhancing fusionpartners. Other fusion partners may be selected so as to increase thesolubility of the polypeptide or to enable the polypeptide to betargeted to desired intracellular compartments. Still further fusionpartners include affinity tags, which facilitate purification of thepolypeptide.

Fusion polypeptides may generally be prepared using standard techniques,including chemical conjugation. Preferably, a fusion polypeptide isexpressed as a recombinant polypeptide, allowing the production ofincreased levels, relative to a non-fused polypeptide, in an expressionsystem. Briefly, DNA sequences encoding the polypeptide components maybe assembled separately, and ligated into an appropriate expressionvector. The 3′ end of the DNA sequence encoding one polypeptidecomponent is ligated, with or without a peptide linker, to the 5′ end ofa DNA sequence encoding the second polypeptide component so that thereading frames of the sequences are in phase. This permits translationinto a single fusion polypeptide that retains the biological activity ofboth component polypeptides.

A peptide linker sequence may be employed to separate the first andsecond polypeptide components by a distance sufficient to ensure thateach polypeptide folds into its secondary and tertiary structures. Sucha peptide linker sequence is incorporated into the fusion polypeptideusing standard techniques well known in the art. Suitable peptide linkersequences may be chosen based on the following factors: (1) theirability to adopt a flexible extended conformation; (2) their inabilityto adopt a secondary structure that could interact with functionalepitopes on the first and second polypeptides; and (3) the lack ofhydrophobic or charged residues that might react with the polypeptidefunctional epitopes. Preferred peptide linker sequences contain Gly, Asnand Ser residues. Other near neutral amino acids, such as Thr and Alamay also be used in the linker sequence. Amino acid sequences which maybe usefully employed as linkers include those disclosed in Maratea etal., Gene 40:39–46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA83:8258–8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180.The linker sequence may generally be from 1 to about 50 amino acids inlength. Linker sequences are not required when the first and secondpolypeptides have non-essential N-terminal amino acid regions that canbe used to separate the functional domains and prevent stericinterference.

The ligated DNA sequences are operably linked to suitabletranscriptional or translational regulatory elements. The regulatoryelements responsible for expression of DNA are located only 5′ to theDNA sequence encoding the first polypeptides. Similarly, stop codonsrequired to end translation and transcription termination signals areonly present 3′ to the DNA sequence encoding the second polypeptide.

The fusion polypeptide can comprise a polypeptide as described hereintogether with an unrelated immunogenic protein, such as an immunogenicprotein capable of eliciting a recall response. Examples of suchproteins include tetanus, tuberculosis and hepatitis proteins (see, forexample, Stoute et al. New Engl. J. Med., 336:86–91, 1997).

In one preferred embodiment, the immunological fusion partner is derivedfrom a Mycobacterium sp., such as a Mycobacterium tuberculosis-derivedRa12 fragment. Ra12 compositions and methods for their use in enhancingthe expression and/or immunogenicity of heterologouspolynucleotide/polypeptide sequences is described in U.S. PatentApplication 60/158,585, the disclosure of which is incorporated hereinby reference in its entirety. Briefly, Ra12 refers to a polynucleotideregion that is a subsequence of a Mycobacterium tuberculosis MTB32Anucleic acid. MTB32A is a serine protease of 32 KD molecular weightencoded by a gene in virulent and avirulent strains of M. tuberculosis.The nucleotide sequence and amino acid sequence of MTB32A have beendescribed (for example, U.S. Patent Application 60/158,585; see also,Skeiky et al., Infection and Immun. (1999) 67:3998–4007, incorporatedherein by reference). C-terminal fragments of the MTB32A coding sequenceexpress at high levels and remain as soluble polypeptides throughout thepurification process. Moreover, Ra12 may enhance the immunogenicity ofheterologous immunogenic polypeptides with which it is fused. Onepreferred Ra12 fusion polypeptide comprises a 14 KD C-terminal fragmentcorresponding to amino acid residues 192 to 323 of MTB32A. Otherpreferred Ra12 polynucleotides generally comprise at least about 15consecutive nucleotides, at least about 30 nucleotides, at least about60 nucleotides, at least about 100 nucleotides, at least about 200nucleotides, or at least about 300 nucleotides that encode a portion ofa Ra12 polypeptide. Ra12 polynucleotides may comprise a native sequence(i.e., an endogenous sequence that encodes a Ra12 polypeptide or aportion thereof) or may comprise a variant of such a sequence. Ra12polynucleotide variants may contain one or more substitutions,additions, deletions and/or insertions such that the biological activityof the encoded fusion polypeptide is not substantially diminished,relative to a fusion polypeptide comprising a native Ra12 polypeptide.Variants preferably exhibit at least about 70% identity, more preferablyat least about 80% identity and most preferably at least about 90%identity to a polynucleotide sequence that encodes a native Ra12polypeptide or a portion thereof.

Within other preferred embodiments, an immunological fusion partner isderived from protein D, a surface protein of the gram-negative bacteriumHaemophilus influenza B (WO 91/18926). Preferably, a protein Dderivative comprises approximately the first third of the protein (e.g.,the first N-terminal 100–110 amino acids), and a protein D derivativemay be lipidated. Within certain preferred embodiments, the first 109residues of a Lipoprotein D fusion partner is included on the N-terminusto provide the polypeptide with additional exogenous T-cell epitopes andto increase the expression level in E. coli (thus functioning as anexpression enhancer). The lipid tail ensures optimal presentation of theantigen to antigen presenting cells. Other fusion partners include thenon-structural protein from influenzae virus, NS 1 (hemaglutinin).Typically, the N-terminal 81 amino acids are used, although differentfragments that include T-helper epitopes may be used.

In another embodiment, the immunological fusion partner is the proteinknown as LYTA, or a portion thereof (preferably a C-terminal portion).LYTA is derived from Streptococcus pneumoniae, which synthesizes anN-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytAgene; Gene 43:265–292, 1986). LYTA is an autolysin that specificallydegrades certain bonds in the peptidoglycan backbone. The C-terminaldomain of the LYTA protein is responsible for the affinity to thecholine or to some choline analogues such as DEAE. This property hasbeen exploited for the development of E. coli C-LYTA expressing plasmidsuseful for expression of fusion proteins. Purification of hybridproteins containing the C-LYTA fragment at the amino terminus has beendescribed (see Biotechnology 10:795–798, 1992). Within a preferredembodiment, a repeat portion of LYTA may be incorporated into a fusionpolypeptide. A repeat portion is found in the C-terminal region startingat residue 178. A particularly preferred repeat portion incorporatesresidues 188–305.

Yet another illustrative embodiment involves fusion polypeptides, andthe polynucleotides encoding them, wherein the fusion partner comprisesa targeting signal capable of directing a polypeptide to theendosomal/lysosomal compartment, as described in U.S. Pat. No.5,633,234. An immunogenic polypeptide of the invention, when fused withthis targeting signal, will associate more efficiently with MHC class IImolecules and thereby provide enhanced in vivo stimulation of CD4⁺T-cells specific for the polypeptide.

WT1 Polynucleotides

Any polynucleotide that encodes a WT1 polypeptide as described herein isa WT1 polynucleotide encompassed by the present invention. Suchpolynucleotides may be single-stranded (coding or antisense) ordouble-stranded, and may be DNA (genomic, cDNA or synthetic) or RNAmolecules. Additional coding or non-coding sequences may, but need not,be present within a polynucleotide of the present invention, and apolynucleotide may, but need not, be linked to other molecules and/orsupport materials.

WT1 polynucleotides may encode a native WT1 protein, or may encode avariant of WT1 as described herein. Polynucleotide variants may containone or more substitutions, additions, deletions and/or insertions suchthat the immunogenicity of the encoded polypeptide is not diminished,relative to a native WT1 protein. The effect on the immunogenicity ofthe encoded polypeptide may generally be assessed as described herein.Preferred variants contain nucleotide substitutions, deletions,insertions and/or additions at no more than 20%, preferably at no morethan 10%, of the nucleotide positions that encode an immunogenic portionof a native WT1 sequence. Certain variants are substantially homologousto a native gene, or a portion thereof. Such polynucleotide variants arecapable of hybridizing under moderately stringent conditions to anaturally occurring DNA sequence encoding a WT1 polypeptide (or acomplementary sequence). Suitable moderately stringent conditionsinclude prewashing in a solution of 5× SSC, 0.5% SDS, 1.0 mM EDTA (pH8.0); hybridizing at 50° C.–65° C., 5× SSC, overnight; followed bywashing twice at 65° C. for 20 minutes with each of 2×, 0.5× and 0.2×SSC containing 0.1% SDS). Such hybridizing DNA sequences are also withinthe scope of this invention.

It will be appreciated by those of ordinary skill in the art that, as aresult of the degeneracy of the genetic code, there are many nucleotidesequences that encode a WT1 polypeptide. Some of these polynucleotidesbear minimal homology to the nucleotide sequence of any native gene.Nonetheless, polynucleotides that vary due to differences in codon usageare specifically contemplated by the present invention.

Once an immunogenic portion of WT1 is identified, as described above, aWT1 polynucleotide may be prepared using any of a variety of techniques.For example, a WT1 polynucleotide may be amplified from cDNA preparedfrom cells that express WT1. Such polynucleotides may be amplified viapolymerase chain reaction (PCR). For this approach, sequence-specificprimers may be designed based on the sequence of the immunogenic portionand may be purchased or synthesized. For example, suitable primers forPCR amplification of a human WT1 gene include: first step—P118:1434–1414: 5′ GAG AGT CAG ACT TGA AAG CAGT 3′ (SEQ ID NO:5) and P135:5′CTG AGC CTC AGC AAA TGG GC 3′ (SEQ ID NO:6); second step—P136: 5′ GAGCAT GCA TGG GCT CCG ACG TGC GGG 3′ (SEQ ID NO:7) and P137: 5′ GGG GTACCC ACT GAA CGG TCC CCG A 3′ (SEQ ID NO:8). Primers for PCRamplification of a mouse WT1 gene include: first step—P138: 5′ TCC GAGCCG CAC CTC ATG 3′ (SEQ ID NO:9) and P139: 5′ GCC TGG GAT GCT GGA CTG 3′(SEQ ID NO:10), second step —P140: 5′ GAG CAT GCG ATG GGT TCC GAC GTGCGG 3′ (SEQ ID NO:11) and P141: 5′ GGG GTA CCT CAA AGC GCC ACG TGG AGTTT 3′ (SEQ ID NO:12).

An amplified portion may then be used to isolate a full length gene froma human genomic DNA library or from a suitable cDNA library, using wellknown techniques. Alternatively, a full length gene can be constructedfrom multiple PCR fragments. WT1 polynucleotides may also be prepared bysynthesizing oligonucleotide components, and ligating componentstogether to generate the complete polynucleotide.

WT1 polynucleotides may also be synthesized by any method known in theart, including chemical synthesis (e.g., solid phase phosphoramiditechemical synthesis). Modifications in a polynucleotide sequence may alsobe introduced using standard mutagenesis techniques, such asoligonucleotide-directed site-specific mutagenesis (see Adelman et al.,DNA 2:183, 1983). Alternatively, RNA molecules may be generated by invitro or in vivo transcription of DNA sequences encoding a WT1polypeptide, provided that the DNA is incorporated into a vector with asuitable RNA polymerase promoter (such as T7 or SP6). Certain portionsmay be used to prepare an encoded polypeptide, as described herein. Inaddition, or alternatively, a portion may be administered to a patientsuch that the encoded polypeptide is generated in vivo (e.g., bytransfecting antigen-presenting cells such as dendritic cells with acDNA construct encoding a WT1 polypeptide, and administering thetransfected cells to the patient).

Polynucleotides that encode a WT1 polypeptide may generally be used forproduction of the polypeptide, in vitro or in vivo. WT1 polynucleotidesthat are complementary to a coding sequence (i.e., antisensepolynucleotides) may also be used as a probe or to inhibit WT1expression. cDNA constructs that can be transcribed into antisense RNAmay also be introduced into cells of tissues to facilitate theproduction of antisense RNA.

Any polynucleotide may be further modified to increase stability invivo. Possible modifications include, but are not limited to, theaddition of flanking sequences at the 5′ and/or 3′ ends; the use ofphosphorothioate or 2′ O-methyl rather than phosphodiesterase linkagesin the backbone; and/or the inclusion of nontraditional bases such asinosine, queosine and wybutosine, as well as acetyl- methyl-, thio- andother modified forms of adenine, cytidine, guanine, thymine and uridine.

Nucleotide sequences as described herein may be joined to a variety ofother nucleotide sequences using established recombinant DNA techniques.For example, a polynucleotide may be cloned into any of a variety ofcloning vectors, including plasmids, phagemids, lambda phage derivativesand cosmids. Vectors of particular interest include expression vectors,replication vectors, probe generation vectors and sequencing vectors. Ingeneral, a vector will contain an origin of replication functional in atleast one organism, convenient restriction endonuclease sites and one ormore selectable markers. Other elements will depend upon the desireduse, and will be apparent to those of ordinary skill in the art.

Within certain embodiments, polynucleotides may be formulated so as topermit entry into a cell of a mammal, and expression therein. Suchformulations are particularly useful for therapeutic purposes, asdescribed below. Those of ordinary skill in the art will appreciate thatthere are many ways to achieve expression of a polynucleotide in atarget cell, and any suitable method may be employed. For example, apolynucleotide may be incorporated into a viral vector such as, but notlimited to, adenovirus, adeno-associated virus, retrovirus, or vacciniaor other pox virus (e.g., avian pox virus). Techniques for incorporatingDNA into such vectors are well known to those of ordinary skill in theart. A retroviral vector may additionally transfer or incorporate a genefor a selectable marker (to aid in the identification or selection oftransduced cells) and/or a targeting moiety, such as a gene that encodesa ligand for a receptor on a specific target cell, to render the vectortarget specific. Targeting may also be accomplished using an antibody,by methods known to those of ordinary skill in the art. cDNA constructswithin such a vector may be used, for example, to transfect human oranimal cell lines for use in establishing WT1 positive tumor modelswhich may be used to perform tumor protection and adoptive immunotherapyexperiments to demonstrate tumor or leukemia-growth inhibition or lysisof such cells.

Other therapeutic formulations for polynucleotides include colloidaldispersion systems, such as macromolecule complexes, nanocapsules,microspheres, beads, and lipid-based systems including oil-in-wateremulsions, micelles, mixed micelles, and liposomes. A preferredcolloidal system for use as a delivery vehicle in vitro and in vivo is aliposome (i.e., an artificial membrane vesicle). The preparation and useof such systems is well known in the art.

Antibodies and Fragments Thereof

The present invention further provides binding agents, such asantibodies and antigen-binding fragments thereof, that specifically bindto a WT1 polypeptide. As used herein, an agent is said to “specificallybind” to a WT1 polypeptide if it reacts at a detectable level (within,for example, an ELISA) with a WT1 polypeptide, and does not reactdetectably with unrelated proteins under similar conditions. As usedherein, “binding” refers to a noncovalent association between twoseparate molecules such that a “complex” is formed. The ability to bindmay be evaluated by, for example, determining a binding constant for theformation of the complex. The binding constant is the value obtainedwhen the concentration of the complex is divided by the product of thecomponent concentrations. In general, two compounds are said to “bind,”in the context of the present invention, when the binding constant forcomplex formation exceeds about 10³ L/mol. The binding constant maybedetermined using methods well known in the art.

Any agent that satisfies the above requirements may be a binding agent.In a preferred embodiment, a binding agent is an antibody or anantigen-binding fragment thereof. Certain antibodies are commerciallyavailable from, for example, Santa Cruz Biotechnology (Santa Cruz,Calif.). Alternatively, antibodies may be prepared by any of a varietyof techniques known to those of ordinary skill in the art. See, e.g.,Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory, 1988. In general, antibodies can be produced by cell culturetechniques, including the generation of monoclonal antibodies asdescribed herein, or via transfection of antibody genes into suitablebacterial or mammalian cell hosts, in order to allow for the productionof recombinant antibodies. In one technique, an immunogen comprising thepolypeptide is initially injected into any of a wide variety of mammals(e.g., mice, rats, rabbits, sheep or goats). In this step, thepolypeptides of this invention may serve as the immunogen withoutmodification. Alternatively, particularly for relatively shortpolypeptides, a superior immune response may be elicited if thepolypeptide is joined to a carrier protein, such as bovine serum albuminor keyhole limpet hemocyanin. The immunogen is injected into the animalhost, preferably according to a predetermined schedule incorporating oneor more booster immunizations, and the animals are bled periodically.Polyclonal antibodies specific for the polypeptide may then be purifiedfrom such antisera by, for example, affinity chromatography using thepolypeptide coupled to a suitable solid support.

Monoclonal antibodies specific for the antigenic polypeptide of interestmay be prepared, for example, using the technique of Kohler andMilstein, Eur. J. Immunol. 6:511–519, 1976, and improvements thereto.Briefly, these methods involve the preparation of immortal cell linescapable of producing antibodies having the desired specificity (i.e.,reactivity with the polypeptide of interest). Such cell lines may beproduced, for example, from spleen cells obtained from an animalimmunized as described above. The spleen cells are then immortalized by,for example, fusion with a myeloma cell fusion partner, preferably onethat is syngeneic with the immunized animal. A variety of fusiontechniques may be employed. For example, the spleen cells and myelomacells may be combined with a nonionic detergent for a few minutes andthen plated at low density on a selective medium that supports thegrowth of hybrid cells, but not myeloma cells. A preferred selectiontechnique uses HAT (hypoxanthine, aminopterin, thymidine) selection.After a sufficient time, usually about 1 to 2 weeks, colonies of hybridsare observed. Single colonies are selected and their culturesupernatants tested for binding activity against the polypeptide.Hybridomas having high reactivity and specificity are preferred.

Monoclonal antibodies may be isolated from the supernatants of growinghybridoma colonies. In addition, various techniques may be employed toenhance the yield, such as injection of the hybridoma cell line into theperitoneal cavity of a suitable vertebrate host, such as a mouse.Monoclonal antibodies may then be harvested from the ascites fluid orthe blood. Contaminants may be removed from the antibodies byconventional techniques, such as chromatography, gel filtration,precipitation, and extraction. The polypeptides of this invention may beused in the purification process in, for example, an affinitychromatography step.

Within certain embodiments, the use of antigen-binding fragments ofantibodies may be preferred. Such fragments include Fab fragments, whichmay be prepared using standard techniques. Briefly, immunoglobulins maybe purified from rabbit serum by affinity chromatography on Protein Abead columns (Harlow and Lane, Antibodies: A Laboratory Manual, ColdSpring Harbor Laboratory, 1988) and digested by papain to yield Fab andFc fragments. The Fab and Fc fragments may be separated by affinitychromatography on protein A bead columns.

Monoclonal antibodies and fragments thereof may be coupled to one ormore therapeutic agents. Suitable agents in this regard includeradioactive tracers and chemotherapeutic agents, which may be used, forexample, to purge autologous bone marrow in vitro). Representativetherapeutic agents include radionuclides, differentiation inducers,drugs, toxins, and derivatives thereof. Preferred radionuclides include⁹⁰Y, ¹²³I, ¹²⁵I, ¹³¹I, ¹⁸⁶Re, ¹⁸⁸Re, ²¹¹At, and ²¹²Bi. Preferred drugsinclude methotrexate, and pyrimidine and purine analogs. Preferreddifferentiation inducers include phorbol esters and butyric acid.Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin,gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviralprotein. For diagnostic purposes, coupling of radioactive agents may beused to facilitate tracing of metastases or to determine the location ofWT1-positive tumors.

A therapeutic agent may be coupled (e.g., covalently bonded) to asuitable monoclonal antibody either directly or indirectly (e.g., via alinker group). A direct reaction between an agent and an antibody ispossible when each possesses a substituent capable of reacting with theother. For example, a nucleophilic group, such as an amino or sulfhydrylgroup, on one may be capable of reacting with a carbonyl-containinggroup, such as an anhydride or an acid halide, or with an alkyl groupcontaining a good leaving group (e.g., a halide) on the other.

Alternatively, it may be desirable to couple a therapeutic agent and anantibody via a linker group. A linker group can function as a spacer todistance an antibody from an agent in order to avoid interference withbinding capabilities. A linker group can also serve to increase thechemical reactivity of a substituent on an agent or an antibody, andthus increase the coupling efficiency. An increase in chemicalreactivity may also facilitate the use of agents, or functional groupson agents, which otherwise would not be possible.

It will be evident to those skilled in the art that a variety ofbifunctional or polyfunctional reagents, both homo- andhetero-functional (such as those described in the catalog of the PierceChemical Co., Rockford, Ill.), may be employed as the linker group.Coupling may be effected, for example, through amino groups, carboxylgroups, sulfhydryl groups or oxidized carbohydrate residues. There arenumerous references describing such methodology, e.g., U.S. Pat. No.4,671,958, to Rodwell et al.

Where a therapeutic agent is more potent when free from the antibodyportion of the immunoconjugates of the present invention, it may bedesirable to use a linker group which is cleavable during or uponinternalization into a cell. A number of different cleavable linkergroups have been described. The mechanisms for the intracellular releaseof an agent from these linker groups include cleavage by reduction of adisulfide bond (e.g., U.S. Pat. No. 4,489,710, to Spitler), byirradiation of a photolabile bond (e.g., U.S. Pat. No. 4,625,014, toSenter et al.), by hydrolysis of derivatized amino acid side chains(e.g., U.S. Pat. No. 4,638,045, to Kohn et al.), by serumcomplement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958, toRodwell et al.), and acid-catalyzed hydrolysis (e.g., U.S. Pat. No.4,569,789, to Blattler et al.).

It may be desirable to couple more than one agent to an antibody. In oneembodiment, multiple molecules of an agent are coupled to one antibodymolecule. In another embodiment, more than one type of agent may becoupled to one antibody. Regardless of the particular embodiment,immunoconjugates with more than one agent may be prepared in a varietyof ways. For example, more than one agent may be coupled directly to anantibody molecule, or linkers which provide multiple sites forattachment can be used. Alternatively, a carrier can be used. A carriermay bear the agents in a variety of ways, including covalent bondingeither directly or via a linker group. Suitable carriers includeproteins such as albumins (e.g., U.S. Pat. No. 4,507,234, to Kato etal.), peptides and polysaccharides such as aminodextran (e.g., U.S. Pat.No. 4,699,784, to Shih et al.). A carrier may also bear an agent bynoncovalent bonding or by encapsulation, such as within a liposomevesicle (e.g., U.S. Pat. Nos. 4,429,008 and 4,873,088). Carriersspecific for radionuclide agents include radiohalogenated smallmolecules and chelating compounds. For example, U.S. Pat. No. 4,735,792discloses representative radiohalogenated small molecules and theirsynthesis. A radionuclide chelate may be formed from chelating compoundsthat include those containing nitrogen and sulfur atoms as the donoratoms for binding the metal, or metal oxide, radionuclide. For example,U.S. Pat. No. 4,673,562, to Davison et al. discloses representativechelating compounds and their synthesis.

A variety of routes of administration for the antibodies andimmunoconjugates may be used. Typically, administration will beintravenous, intramuscular, subcutaneous or in the bed of a resectedtumor. It will be evident that the precise dose of theantibody/immunoconjugate will vary depending upon the antibody used, theantigen density on the tumor, and the rate of clearance of the antibody.

Also provided herein are anti-idiotypic antibodies that mimic animmunogenic portion of WT1. Such antibodies may be raised against anantibody, or antigen-binding fragment thereof, that specifically bindsto an immunogenic portion of WT1, using well known techniques.Anti-idiotypic antibodies that mimic an immunogenic portion of WT1 arethose antibodies that bind to an antibody, or antigen-binding fragmentthereof, that specifically binds to an immunogenic portion of WT1, asdescribed herein.

T Cells

Immunotherapeutic compositions may also, or alternatively, comprise Tcells specific for WT1. Such cells may generally be prepared in vitro orex vivo, using standard procedures. For example, T cells may be presentwithin (or isolated from) bone marrow, peripheral blood or a fraction ofbone marrow or peripheral blood of a mammal, such as a patient, using acommercially available cell separation system, such as the CEPRATE™system, available from CellPro Inc., Bothell Wash. (see also U.S. Pat.No. 5,240,856; U.S. Pat. No. 5,215,926; WO 89/06280; WO 91/16116 and WO92/07243). Alternatively, T cells may be derived from related orunrelated humans, non-human animals, cell lines or cultures.

T cells may be stimulated with WT1 polypeptide, polynucleotide encodinga WT1 polypeptide and/or an antigen presenting cell (APC) that expressesa WT1 polypeptide. Such stimulation is performed under conditions andfor a time sufficient to permit the generation of T cells that arespecific for the WT1 polypeptide. Preferably, a WT1 polypeptide orpolynucleotide is present within a delivery vehicle, such as amicrosphere, to facilitate the generation of antigen-specific T cells.Briefly, T cells, which may be isolated from a patient or a related orunrelated donor by routine techniques (such as by Ficoll/Hypaque densitygradient centrifugation of peripheral blood lymphocytes), are incubatedwith WT1 polypeptide. For example, T cells may be incubated in vitro for2–9 days (typically 4 days) at 37° C. with WT1 polypeptide (e.g., 5 to25 μg/ml) or cells synthesizing a comparable amount of WT1 polypeptide.It may be desirable to incubate a separate aliquot of a T cell sample inthe absence of WT1 polypeptide to serve as a control.

T cells are considered to be specific for a WT1 polypeptide if the Tcells kill target cells coated with a WT1 polypeptide or expressing agene encoding such a polypeptide. T cell specificity may be evaluatedusing any of a variety of standard techniques. For example, within achromium release assay or proliferation assay, a stimulation index ofmore than two fold increase in lysis and/or proliferation, compared tonegative controls, indicates T cell specificity. Such assays may beperformed, for example, as described in Chen et al., Cancer Res.54:1065–1070, 1994. Alternatively, detection of the proliferation of Tcells may be accomplished by a variety of known techniques. For example,T cell proliferation can be detected by measuring an increased rate ofDNA synthesis (e.g., by pulse-labeling cultures of T cells withtritiated thymidine and measuring the amount of tritiated thymidineincorporated into DNA). Other ways to detect T cell proliferationinclude measuring increases in interleukin-2 (IL-2) production, Ca²⁺flux, or dye uptake, such as3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium. Alternatively,synthesis of lymphokines (such as interferon-gamma) can be measured orthe relative number of T cells that can respond to a WT1 polypeptide maybe quantified. Contact with a WT1 polypeptide (200 ng/ml–100 μg/ml,preferably 100 ng/ml–25 μg/ml) for 3–7 days should result in at least atwo fold increase in proliferation of the T cells and/or contact asdescribed above for 2–3 hours should result in activation of the Tcells, as measured using standard cytokine assays in which a two foldincrease in the level of cytokine release (e.g., TNF or IFN-γ) isindicative of T cell activation (see Coligan et al., Current Protocolsin Immunology, vol. 1, Wiley Interscience (Greene 1998). WT1 specific Tcells may be expanded using standard techniques. Within preferredembodiments, the T cells are derived from a patient or a related orunrelated donor and are administered to the patient followingstimulation and expansion.

T cells that have been activated in response to a WT1 polypeptide,polynucleotide or WT1-expressing APC may be CD4⁺ and/or CD8⁺. Specificactivation of CD4⁺ or CD8⁺ T cells may be detected in a variety of ways.Methods for detecting specific T cell activation include detecting theproliferation of T cells, the production of cytokines (e.g.,lymphokines), or the generation of cytolytic activity (i.e., generationof cytotoxic T cells specific for WT1). For CD4⁺ T cells, a preferredmethod for detecting specific T cell activation is the detection of theproliferation of T cells. For CD8⁺ T cells, a preferred method fordetecting specific T cell activation is the detection of the generationof cytolytic activity.

For therapeutic purposes, CD4⁺ or CD8⁺ T cells that proliferate inresponse to the WT1 polypeptide, polynucleotide or APC can be expandedin number either in vitro or in vivo. Proliferation of such T cells invitro may be accomplished in a variety of ways. For example, the T cellscan be re-exposed to WT1 polypeptide, with or without the addition of Tcell growth factors, such as interleukin-2, and/or stimulator cells thatsynthesize a WT1 polypeptide. The addition of stimulator cells ispreferred where generating CD8⁺ T cell responses. T cells can be grownto large numbers in vitro with retention of specificity in response tointermittent restimulation with WT1 polypeptide. Briefly, for theprimary in vitro stimulation (IVS), large numbers of lymphocytes (e.g.,greater than 4×10⁷) may be placed in flasks with media containing humanserum. WT1 polypeptide (e.g., peptide at 10 μg/ml) may be addeddirectly, along with tetanus toxoid (e.g., 5 μg/ml). The flasks may thenbe incubated (e.g., 37° C. for 7 days). For a second IVS, T cells arethen harvested and placed in new flasks with 2–3×10⁷ irradiatedperipheral blood mononuclear cells. WT1 polypeptide (e.g., 10 μg/ml) isadded directly. The flasks are incubated at 37° C. for 7 days. On day 2and day 4 after the second IVS, 2–5 units of interleukin-2 (IL-2) may beadded. For a third IVS, the T cells may be placed in wells andstimulated with the individual's own EBV transformed B cells coated withthe peptide. IL-2 may be added on days 2 and 4 of each cycle. As soon asthe cells are shown to be specific cytotoxic T cells, they may beexpanded using a 10 day stimulation cycle with higher IL-2 (20 units) ondays 2, 4 and 6.

Alternatively, one or more T cells that proliferate in the presence ofWT1 polypeptide can be expanded in number by cloning. Methods forcloning cells are well known in the art, and include limiting dilution.Responder T cells may be purified from the peripheral blood ofsensitized patients by density gradient centrifugation and sheep redcell rosetting and established in culture by stimulating with thenominal antigen in the presence of irradiated autologous filler cells.In order to generate CD4⁺ T cell lines, WT1 polypeptide is used as theantigenic stimulus and autologous peripheral blood lymphocytes (PBL) orlymphoblastoid cell lines (LCL) immortalized by infection with EpsteinBarr virus are used as antigen presenting cells. In order to generateCD8⁺ T cell lines, autologous antigen-presenting cells transfected withan expression vector which produces WT1 polypeptide may be used asstimulator cells. Established T cell lines may be cloned 2–4 daysfollowing antigen stimulation by plating stimulated T cells at afrequency of 0.5 cells per well in 96-well flat-bottom plates with 1×10⁶irradiated PBL or LCL cells and recombinant interleukin-2 (rIL2) (50U/ml). Wells with established clonal growth may be identified atapproximately 2–3 weeks after initial plating and restimulated withappropriate antigen in the presence of autologous antigen-presentingcells, then subsequently expanded by the addition of low doses of rIL2(10 U/ml) 2–3 days following antigen stimulation. T cell clones may bemaintained in 24-well plates by periodic restimulation with antigen andrIL2 approximately every two weeks.

Within certain embodiments, allogeneic T-cells may be primed (i.e.,sensitized to WT1) in vivo and/or in vitro. Such priming may be achievedby contacting T cells with a WT1 polypeptide, a polynucleotide encodingsuch a polypeptide or a cell producing such a polypeptide underconditions and for a time sufficient to permit the priming of T cells.In general, T cells are considered to be primed if, for example, contactwith a WT1 polypeptide results in proliferation and/or activation of theT cells, as measured by standard proliferation, chromium release and/orcytokine release assays as described herein. A stimulation index of morethan two fold increase in proliferation or lysis, and more than threefold increase in the level of cytokine, compared to negative controls,indicates T-cell specificity. Cells primed in vitro may be employed, forexample, within a bone marrow transplantation or as donor lymphocyteinfusion.

Pharmaceutical Compositions and Vaccines

Within certain aspects, polypeptides, polynucleotides, antibodies and/orT cells may be incorporated into pharmaceutical compositions orvaccines. Alternatively, a pharmaceutical composition may comprise anantigen-presenting cell (e.g., a dendritic cell) transfected with a WT1polynucleotide such that the antigen presenting cell expresses a WT1polypeptide. Pharmaceutical compositions comprise one or more suchcompounds or cells and a physiologically acceptable carrier orexcipient. Certain vaccines may comprise one or more such compounds orcells and a non-specific immune response enhancer, such as an adjuvantor a liposome (into which the compound is incorporated). Pharmaceuticalcompositions and vaccines may additionally contain a delivery system,such as biodegradable microspheres which are disclosed, for example, inU.S. Pat. Nos. 4,897,268 and 5,075,109. Pharmaceutical compositions andvaccines within the scope of the present invention may also containother compounds, which may be biologically active or inactive.

Within certain embodiments, pharmaceutical compositions and vaccines aredesigned to elicit T cell responses specific for a WT1 polypeptide in apatient, such as a human. In general, T cell responses may be favoredthrough the use of relatively short polypeptides (e.g., comprising lessthan 23 consecutive amino acid residues of a native WT1 polypeptide,preferably 4–16 consecutive residues, more preferably 8–16 consecutiveresidues and still more preferably 8–10 consecutive residues.Alternatively, or in addition, a vaccine may comprise a non-specificimmune response enhancer that preferentially enhances a T cell response.In other words, the immune response enhancer may enhance the level of aT cell response to a WT1 polypeptide by an amount that is proportionallygreater than the amount by which an antibody response is enhanced. Forexample, when compared to a standard oil based adjuvant, such as CFA, animmune response enhancer that preferentially enhances a T cell responsemay enhance a proliferative T cell response by at least two fold, alytic response by at least 10%, and/or T cell activation by at least twofold compared to WT1-megative control cell lines, while not detectablyenhancing an antibody response. The amount by which a T cell or antibodyresponse to a WT1 polypeptide is enhanced may generally be determinedusing any representative technique known in the art, such as thetechniques provided herein.

A pharmaceutical composition or vaccine may contain DNA encoding one ormore of the polypeptides as described above, such that the polypeptideis generated in situ. As noted above, the DNA may be present within anyof a variety of delivery systems known to those of ordinary skill in theart, including nucleic acid expression systems, bacterial and viralexpression systems and mammalian expression systems. Appropriate nucleicacid expression systems contain the necessary DNA, cDNA or RNA sequencesfor expression in the patient (such as a suitable promoter andterminating signal). Bacterial delivery systems involve theadministration of a bacterium (such as Bacillus-Calmette-Guerrin) thatexpresses an immunogenic portion of the polypeptide on its cell surface.In a preferred embodiment, the DNA may be introduced using a viralexpression system (e.g., vaccinia or other pox virus, retrovirus, oradenovirus), which may involve the use of a non-pathogenic (defective),replication competent virus. Techniques for incorporating DNA into suchexpression systems are well known to those of ordinary skill in the art.The DNA may also be “naked,” as described, for example, in Ulmer et al.,Science 259:1745–1749, 1993 and reviewed by Cohen, Science259:1691–1692, 1993. The uptake of naked DNA may be increased by coatingthe DNA onto biodegradable beads, which are efficiently transported intothe cells.

As noted above, a pharmaceutical composition or vaccine may comprise anantigen-presenting cell that expresses a WT1 polypeptide. Fortherapeutic purposes, as described herein, the antigen presenting cellis preferably an autologous dendritic cell. Such cells may be preparedand transfected using standard techniques, such as those described byReeves et al., Cancer Res. 56:5672–5677, 1996; Tuting et al., J.Immunol. 160:1139–1147, 1998; and Nair et al., Nature Biotechnol.16:364–369, 1998). Expression of a WT1 polypeptide on the surface of anantigen-presenting cell may be confirmed by in vitro stimulation andstandard proliferation as well as chromium release assays, as describedherein.

While any suitable carrier known to those of ordinary skill in the artmay be employed in the pharmaceutical compositions of this invention,the type of carrier will vary depending on the mode of administration.Compositions of the present invention may be formulated for anyappropriate manner of administration, including for example, topical,oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous orintramuscular administration. For parenteral administration, such assubcutaneous injection, the carrier preferably comprises water, saline,alcohol, a fat, a wax or a buffer. For oral administration, any of theabove carriers or a solid carrier, such as mannitol, lactose, starch,magnesium stearate, sodium saccharine, talcum, cellulose, glucose,sucrose, and magnesium carbonate, may be employed. Biodegradablemicrospheres (e.g., polylactate polyglycolate) may also be employed ascarriers for the pharmaceutical compositions of this invention. Forcertain topical applications, formulation as a cream or lotion, usingwell known components, is preferred.

Such compositions may also comprise buffers (e.g., neutral bufferedsaline or phosphate buffered saline), carbohydrates (e.g., glucose,mannose, sucrose or dextrans), mannitol, proteins, polypeptides or aminoacids such as glycine, antioxidants, chelating agents such as EDTA orglutathione, adjuvants (e.g., aluminum hydroxide) and/or preservatives.Alternatively, compositions of the present invention may be formulatedas a lyophilizate. Compounds may also be encapsulated within liposomesusing well known technology.

Any of a variety of non-specific immune response enhancers, such asadjuvants, may be employed in the vaccines of this invention. Mostadjuvants contain a substance designed to protect the antigen from rapidcatabolism, such as aluminum hydroxide or mineral oil, and a stimulatorof immune responses, such as lipid A, Bortadella pertussis orMycobacterium tuberculosis derived proteins. Suitable non-specificimmune response enhancers include alum-based adjuvants (e.g.,Alhydrogel, Rehydragel, aluminum phosphate, Algammulin, aluminumhydroxide); oil based adjuvants (Freund's adjuvant (FA), Specol, RIBI,TiterMax, Montanide ISA50 or Seppic MONTANIDE ISA 720; cytokines (e.g.,GM-CSF or Flat3-ligand); microspheres; nonionic block copolymer-basedadjuvants; dimethyl dioctadecyl ammoniumbromide (DDA) based adjuvantsAS-1, AS-2 (Smith Kline Beecham); Ribi Adjuvant system based adjuvants;QS21 (Aquila); saponin based adjuvants (crude saponin, the saponin QuilA); muramyl dipeptide (MDP) based adjuvants such as SAF (Syntex adjuvantin its microfluidized form (SAF-m)); dimethyl-dioctadecyl ammoniumbromide (DDA); human complement based adjuvants m. vaccae andderivatives; immune stimulating complex (iscom) based adjuvants;inactivated toxins; and attenuated infectious agents (such as M.tuberculosis).

As noted above, within certain embodiments, immune response enhancersare chosen for their ability to preferentially elicit or enhance a Tcell response (e.g., CD4⁺ and/or CD8⁺) to a WT1 polypeptide. Such immuneresponse enhancers are well known in the art, and include (but are notlimited to) Montanide ISA50, Seppic MONTANIDE ISA 720, cytokines (e.g.,GM-CSF, Flat3-ligand), microspheres, dimethyl dioctadecylammoniumbromide (DDA) based adjuvants, AS-1 (Smith Kline Beecham), AS-2(Smith Kline Beecham), Ribi Adjuvant system based adjuvants, QS21(Aquila), saponin based adjuvants (crude saponin, the saponin Quil A),Syntex adjuvant in its microfluidized form (SAF-m), MV, ddMV (Genesis),immune stimulating complex (iscom) based adjuvants and inactivatedtoxins.

The compositions and vaccines described herein may be administered aspart of a sustained release formulation (i.e., a formulation such as acapsule or sponge that effects a slow release of compound followingadministration). Such formulations may generally be prepared using wellknown technology and administered by, for example, oral, rectal orsubcutaneous implantation, or by implantation at the desired targetsite. Sustained-release formulations may contain a polypeptide,polynucleotide, antibody or cell dispersed in a carrier matrix and/orcontained within a reservoir surrounded by a rate controlling membrane.Carriers for use within such formulations are biocompatible, and mayalso be biodegradable; preferably the formulation provides a relativelyconstant level of active component release. The amount of activecompound contained within a sustained release formulation depends uponthe site of implantation, the rate and expected duration of release andthe nature of the condition to be treated or prevented.

Therapy of Malignant Diseases

In further aspects of the present invention, the compositions andvaccines described herein may be used to inhibit the development ofmalignant diseases (e.g., progressive or metastatic diseases or diseasescharacterized by small tumor burden such as minimal residual disease).In general, such methods may be used to prevent, delay or treat adisease associated with WT1 expression. In other words, therapeuticmethods provided herein may be used to treat an existing WT1-associateddisease, or may be used to prevent or delay the onset of such a diseasein a patient who is free of disease or who is afflicted with a diseasethat is not yet associated with WT1 expression.

As used herein, a disease is “associated with WT1 expression” ifdiseased cells (e.g., tumor cells) at some time during the course of thedisease generate detectably higher levels of a WT1 polypeptide thannormal cells of the same tissue. Association of WT1 expression with amalignant disease does not require that WT1 be present on a tumor. Forexample, overexpression of WT1 may be involved with initiation of atumor, but the protein expression may subsequently be lost.Alternatively, a malignant disease that is not characterized by anincrease in WT1 expression may, at a later time, progress to a diseasethat is characterized by increased WT1 expression. Accordingly, anymalignant disease in which diseased cells formerly expressed, currentlyexpress or are expected to subsequently express increased levels of WT1is considered to be “associated with WT1 expression.”

Immunotherapy may be performed using any of a variety of techniques, inwhich compounds or cells provided herein function to removeWT1-expressing cells from a patient. Such removal may take place as aresult of enhancing or inducing an immune response in a patient specificfor WT1 or a cell expressing WT1. Alternatively, WT1-expressing cellsmay be removed ex vivo (e.g., by treatment of autologous bone marrow,peripheral blood or a fraction of bone marrow or peripheral blood).Fractions of bone marrow or peripheral blood may be obtained using anystandard technique in the art.

Within such methods, pharmaceutical compositions and vaccines may beadministered to a patient. As used herein, a “patient” refers to anywarm-blooded animal, preferably a human. A patient may or may not beafflicted with a malignant disease. Accordingly, the abovepharmaceutical compositions and vaccines may be used to prevent theonset of a disease (i.e., prophylactically) or to treat a patientafflicted with a disease (e.g., to prevent or delay progression and/ormetastasis of an existing disease). A patient afflicted with a diseasemay have a minimal residual disease (e.g., a low tumor burden in aleukemia patient in complete or partial remission or a cancer patientfollowing reduction of the tumor burden after surgery radiotherapyand/or chemotherapy). Such a patient may be immunized to inhibit arelapse (i.e., prevent or delay the relapse, or decrease the severity ofa relapse). Within certain preferred embodiments, the patient isafflicted with a leukemia (e.g., AML, CML, ALL or childhood ALL), amyelodysplastic syndrome (MDS) or a cancer (e.g., gastrointestinal,lung, thyroid or breast cancer or a melanoma), where the cancer orleukemia is WT1 positive (i.e., reacts detectably with an anti-WT1antibody, as provided herein or expresses WT1 mRNA at a level detectableby RT-PCR, as described herein) or suffers from an autoimmune diseasedirected against WT1-expressing cells.

Other diseases associated with WT1 overexpression include kidney cancer(such as renal cell carcinoma, or Wilms tumor), as described in SatohF., et al., Pathol. Int. 50(6):458–71(2000), and Campbell C. E. et al.,Int. J. Cancer 78(2):182–8 (1998); and mesothelioma, as described inAmin, K. M. et al., Am. J. Pathol. 146(2):344–56 (1995). Harada et al.(Mol. Urol. 3(4):357–364 (1999) describe WT1 gene expression in humantesticular germ-cell tumors. Nonomura et al. Hinyokika Kiyo 45(8):593–7(1999) describe molecular staging of testicular cancer using polymerasechain reaction of the testicular cancer-specific genes. Shimizu et al.,Int. J. Gynecol. Pathol. 19(2):158–63 (2000) describe theimmunohistochemical detection of the Wilms' tumor gene (WT1) inepithelial ovarian tumors.

WT1 overexpression was also described in desmoplastic small round celltumors, by Barnoud, R. et al., Am. J. Surg. Pathol. 24(6):830–6 (2000);and Pathol. Res. Pract. 194(10):693–700 (1998). WT1 overexpression inglioblastoma and other cancer was described by Menssen, H. D. et al., J.Cancer Res. Clin. Oncol. 126(4):226–32 (2000), “Wilms' tumor gene (WT1)expression in lung cancer, colon cancer and glioblastoma cell linescompared to freshly isolated tumor specimens.” Other diseases showingWT1 overexpression include EBV associated diseases, such as Burkitt'slymphoma and nasopharyngeal cancer (Spinsanti P. et al., Leuk. Lymphoma38(5–6):611–9 (2000), “Wilms' tumor gene expression by normal andmalignant human B lymphocytes.”

In Leukemia 14(9): 1634–4 (2000), Pan et al., describe in vitro IL-12treatment of peripheral blood mononuclear cells from patients withleukemia or myelodysplastic syndromes, and reported an increase incytotoxicity and reduction in WT1 gene expression. In Leukemia13(6):891–900 (1999), Patmasiriwat et al. reported WT1 and GATA1expression in myelodysplastic syndrome and acute leukemia. In Leukemia13(3):393–9 (1999), Tamaki et al. reported that the Wilms' tumor geneWT1 is a good marker for diagnosis of disease progression ofmyelodysplastic syndromes. Expression of the Wilms' tumor gene WT1 insolid tumors, and its involvement in tumor cell growth, was discussed inrelation to gastric cancer, colon cancer, lung cancer, breast cancercell lines, germ cell tumor cell line, ovarian cancer, the uterinecancer, thyroid cancer cell line, hepatocellular carcinoma, in Oji etal., Jpn. J. Cancer Res. 90(2):194–204 (1999).

The compositions provided herein may be used alone or in combinationwith conventional therapeutic regimens such as surgery, irradiation,chemotherapy and/or bone marrow transplantation (autologous, syngeneic,allogeneic or unrelated). As discussed in greater detail below, bindingagents and T cells as provided herein may be used for purging ofautologous stem cells. Such purging may be beneficial prior to, forexample, bone marrow transplantation or transfusion of blood orcomponents thereof. Binding agents, T cells, antigen presenting cells(APC) and compositions provided herein may further be used for expandingand stimulating (or priming) autologous, allogeneic, syngeneic orunrelated WT1-specific T-cells in vitro and/or in vivo. SuchWT1-specific T cells may be used, for example, within donor lymphocyteinfusions.

Routes and frequency of administration, as well as dosage, will varyfrom individual to individual, and may be readily established usingstandard techniques. In general, the pharmaceutical compositions andvaccines may be administered by injection (e.g., intracutaneous,intramuscular, intravenous or subcutaneous), intranasally (e.g., byaspiration) or orally. In some tumors, pharmaceutical compositions orvaccines may be administered locally (by, for example, rectocoloscopy,gastroscopy, videoendoscopy, angiography or other methods known in theart). Preferably, between 1 and 10 doses may be administered over a 52week period. Preferably, 6 doses are administered, at intervals of 1month, and booster vaccinations may be given periodically thereafter.Alternate protocols may be appropriate for individual patients. Asuitable dose is an amount of a compound that, when administered asdescribed above, is capable of promoting an anti-tumor immune responsethat is at least 10–50% above the basal (i.e., untreated) level. Suchresponse can be monitored by measuring the anti-tumor antibodies in apatient or by vaccine-dependent generation of cytolytic effector cellscapable of killing the patient's tumor cells in vitro. Such vaccinesshould also be capable of causing an immune response that leads to animproved clinical outcome (e.g., more frequent complete or partialremissions, or longer disease-free and/or overall survival) invaccinated patients as compared to non-vaccinated patients. In general,for pharmaceutical compositions and vaccines comprising one or morepolypeptides, the amount of each polypeptide present in a dose rangesfrom about 100 μg to 5 mg. Suitable dose sizes will vary with the sizeof the patient, but will typically range from about 0.1 mL to about 5mL.

In general, an appropriate dosage and treatment regimen provides theactive compound(s) in an amount sufficient to provide therapeutic and/orprophylactic benefit. Such a response can be monitored by establishingan improved clinical outcome (e.g., more frequent complete or partialremissions, or longer disease-free and/or overall survival) in treatedpatients as compared to non-treated patients. Increases in preexistingimmune responses to WT1 generally correlate with an improved clinicaloutcome. Such immune responses may generally be evaluated using standardproliferation, cytotoxicity or cytokine assays, which may be performedusing samples obtained from a patient before and after treatment.

Within further aspects, methods for inhibiting the development of amalignant disease associated with WT1 expression involve theadministration of autologous T cells that have been activated inresponse to a WT1 polypeptide or WT1-expressing APC, as described above.Such T cells may be CD4⁺ and/or CD8⁺, and may be proliferated asdescribed above. The T cells may be administered to the individual in anamount effective to inhibit the development of a malignant disease.Typically, about 1×10⁹ to 1×10¹¹ T cells/M² are administeredintravenously, intracavitary or in the bed of a resected tumor. It willbe evident to those skilled in the art that the number of cells and thefrequency of administration will be dependent upon the response of thepatient.

Within certain embodiments, T cells may be stimulated prior to anautologous bone marrow transplantation. Such stimulation may take placein vivo or in vitro. For in vitro stimulation, bone marrow and/orperipheral blood (or a fraction of bone marrow or peripheral blood)obtained from a patient may be contacted with a WT1 polypeptide, apolynucleotide encoding a WT1 polypeptide and/or an APC that expresses aWT1 polypeptide under conditions and for a time sufficient to permit thestimulation of T cells as described above. Bone marrow, peripheral bloodstem cells and/or WT1-specific T cells may then be administered to apatient using standard techniques.

Within related embodiments, T cells of a related or unrelated donor maybe stimulated prior to a syngeneic or allogeneic (related or unrelated)bone marrow transplantation. Such stimulation may take place in vivo orin vitro. For in vitro stimulation, bone marrow and/or peripheral blood(or a fraction of bone marrow or peripheral blood) obtained from arelated or unrelated donor may be contacted with a WT1 polypeptide, WT1polynucleotide and/or APC that expresses a WT1 polypeptide underconditions and for a time sufficient to permit the stimulation of Tcells as described above. Bone marrow, peripheral blood stem cellsand/or WT1-specific T cells may then be administered to a patient usingstandard techniques.

Within other embodiments, WT1-specific T cells as described herein maybe used to remove cells expressing WT1 from autologous bone marrow,peripheral blood or a fraction of bone marrow or peripheral blood (e.g.,CD34⁺ enriched peripheral blood (PB) prior to administration to apatient). Such methods may be performed by contacting bone marrow or PBwith such T cells under conditions and for a time sufficient to permitthe reduction of WT1 expressing cells to less than 10%, preferably lessthan 5% and more preferably less than 1%, of the total number of myeloidor lymphatic cells in the bone marrow or peripheral blood. The extent towhich such cells have been removed may be readily determined by standardmethods such as, for example, qualitative and quantitative PCR analysis,morphology, immunohistochemistry and FACS analysis. Bone marrow or PB(or a fraction thereof) may then be administered to a patient usingstandard techniques.

Diagnostic Methods

The present invention further provides methods for detecting a malignantdisease associated with WT1 expression, and for monitoring theeffectiveness of an immunization or therapy for such a disease. Suchmethods are based on the discovery, within the present invention, thatan immune response specific for WT1 protein can be detected in patientsafflicted with such diseases, and that methods which enhance such immuneresponses may provide a preventive or therapeutic benefit.

To determine the presence or absence of a malignant disease associatedwith WT1 expression, a patient may be tested for the level of T cellsspecific for WT1. Within certain methods, a biological sample comprisingCD4⁺ and/or CD8⁺ T cells isolated from a patient is incubated with a WT1polypeptide, a polynucleotide encoding a WT1 polypeptide and/or an APCthat expresses a WT1 polypeptide, and the presence or absence ofspecific activation of the T cells is detected, as described herein.Suitable biological samples include, but are not limited to, isolated Tcells. For example, T cells may be isolated from a patient by routinetechniques (such as by Ficoll/Hypaque density gradient centrifugation ofperipheral blood lymphocytes). T cells may be incubated in vitro for 2–9days (typically 4 days) at 37° C. with WT1 polypeptide (e.g., 5–25μg/ml). It may be desirable to incubate another aliquot of a T cellsample in the absence of WT1 polypeptide to serve as a control. For CD4⁺T cells, activation is preferably detected by evaluating proliferationof the T cells. For CD8⁺ T cells, activation is preferably detected byevaluating cytolytic activity. A level of proliferation that is at leasttwo fold greater and/or a level of cytolytic activity that is at least20% greater than in disease-free patients indicates the presence of amalignant disease associated with WT1 expression. Further correlationmay be made, using methods well known in the art, between the level ofproliferation and/or cytolytic activity and the predicted response totherapy. In particular, patients that display a higher antibody,proliferative and/or lytic response may be expected to show a greaterresponse to therapy.

Within other methods, a biological sample obtained from a patient istested for the level of antibody specific for WT1. The biological sampleis incubated with a WT1 polypeptide, a polynucleotide encoding a WT1polypeptide and/or an APC that expresses a WT1 polypeptide underconditions and for a time sufficient to allow immunocomplexes to form.Immunocomplexes formed between the WT1 polypeptide and antibodies in thebiological sample that specifically bind to the WT1 polypeptide are thendetected. A biological sample for use within such methods may be anysample obtained from a patient that would be expected to containantibodies. Suitable biological samples include blood, sera, ascites,bone marrow, pleural effusion, and cerebrospinal fluid.

The biological sample is incubated with the WT1 polypeptide in areaction mixture under conditions and for a time sufficient to permitimmunocomplexes to form between the polypeptide and antibodies specificfor WT1. For example, a biological sample and WT1 polypeptide may beincubated at 4° C. for 24–48 hours.

Following the incubation, the reaction mixture is tested for thepresence of immunocomplexes. Detection of immunocomplexes formed betweenthe WT1 polypeptide and antibodies present in the biological sample maybe accomplished by a variety of known techniques, such asradioimmunoassays (RIA) and enzyme linked immunosorbent assays (ELISA).Suitable assays are well known in the art and are amply described in thescientific and patent literature (e.g., Harlow and Lane, Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory, 1988). Assays that maybe used include, but are not limited to, the double monoclonal antibodysandwich immunoassay technique of David et al. (U.S. Pat. No.4,376,110); monoclonal-polyclonal antibody sandwich assays (Wide et al.,in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S.Livingstone, Edinburgh, 1970); the “western blot” method of Gordon etal. (U.S. Pat. No. 4,452,901); immunoprecipitation of labeled ligand(Brown et al., J. Biol. Chem. 255:4980–4983, 1980); enzyme-linkedimmunosorbent assays as described by, for example, Raines and Ross (J.Biol. Chem. 257:5154–5160, 1982); immunocytochemical techniques,including the use of fluorochromes (Brooks et al., Clin. Exp. Immunol.39: 477, 1980); and neutralization of activity (Bowen-Pope et al., Proc.Natl. Acad. Sci. USA 81:2396–2400, 1984). Other immunoassays include,but are not limited to, those described in U.S. Pat. Nos. 3,817,827;3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and4,098,876.

For detection purposes, WT1 polypeptide may either be labeled orunlabeled. Unlabeled WT1 polypeptide may be used in agglutination assaysor in combination with labeled detection reagents that bind to theimmunocomplexes (e.g., anti-immunoglobulin, protein G, protein A or alectin and secondary antibodies, or antigen-binding fragments thereof,capable of binding to the antibodies that specifically bind to the WT1polypeptide). If the WT1 polypeptide is labeled, the reporter group maybe any suitable reporter group known in the art, includingradioisotopes, fluorescent groups, luminescent groups, enzymes, biotinand dye particles.

Within certain assays, unlabeled WT1 polypeptide is immobilized on asolid support. The solid support may be any material known to those ofordinary skill in the art to which the polypeptide may be attached. Forexample, the solid support may be a test well in a microtiter plate or anitrocellulose or other suitable membrane. Alternatively, the supportmay be a bead or disc, such as glass, fiberglass, latex or a plasticmaterial such as polystyrene or polyvinylchloride. The support may alsobe a magnetic particle or a fiber optic sensor, such as those disclosed,for example, in U.S. Pat. No. 5,359,681. The polypeptide may beimmobilized on the solid support using a variety of techniques known tothose of skill in the art, which are amply described in the patent andscientific literature. In the context of the present invention, the term“immobilization” refers to both noncovalent association, such asadsorption, and covalent attachment (which may be a direct linkagebetween the antigen and functional groups on the support or may be alinkage by way of a cross-linking agent). Immobilization by adsorptionto a well in a microtiter plate or to a membrane is preferred. In suchcases, adsorption may be achieved by contacting the WT1 polypeptide, ina suitable buffer, with the solid support for a suitable amount of time.The contact time varies with temperature, but is typically between about1 hour and about 1 day. In general, contacting a well of a plasticmicrotiter plate (such as polystyrene or polyvinylchloride) with anamount of polypeptide ranging from about 10 ng to about 10 μg, andpreferably about 100 ng to about 1 μg, is sufficient to immobilize anadequate amount of polypeptide.

Following immobilization, the remaining protein binding sites on thesupport are typically blocked. Any suitable blocking agent known tothose of ordinary skill in the art, such as bovine serum albumin, Tween20™ (Sigma Chemical Co., St. Louis, Mo.), heat-inactivated normal goatserum (NGS), or BLOTTO (buffered solution of nonfat dry milk which alsocontains a preservative, salts, and an antifoaming agent). The supportis then incubated with a biological sample suspected of containingspecific antibody. The sample can be applied neat, or, more often, itcan be diluted, usually in a buffered solution which contains a smallamount (0.1%–5.0% by weight) of protein, such as BSA, NGS, or BLOTTO. Ingeneral, an appropriate contact time (i.e., incubation time) is a periodof time that is sufficient to detect the presence of antibody thatspecifically binds WT1 within a sample containing such an antibody.Preferably, the contact time is sufficient to achieve a level of bindingthat is at least about 95% of that achieved at equilibrium between boundand unbound antibody. Those of ordinary skill in the art will recognizethat the time necessary to achieve equilibrium may be readily determinedby assaying the level of binding that occurs over a period of time. Atroom temperature, an incubation time of about 30 minutes is generallysufficient.

Unbound sample may then be removed by washing the solid support with anappropriate buffer, such as PBS containing 0.1% Tween 20™. A detectionreagent that binds to the immunocomplexes and that comprises a reportergroup may then be added. The detection reagent is incubated with theimmunocomplex for an amount of time sufficient to detect the boundantibody. An appropriate amount of time may generally be determined byassaying the level of binding that occurs over a period of time. Unbounddetection reagent is then removed and bound detection reagent isdetected using the reporter group. The method employed for detecting thereporter group depends upon the nature of the reporter group. Forradioactive groups, scintillation counting or autoradiographic methodsare generally appropriate. Spectroscopic methods may be used to detectdyes, luminescent groups and fluorescent groups. Biotin may be detectedusing avidin, coupled to a different reporter group (commonly aradioactive or fluorescent group or an enzyme). Enzyme reporter groups(e.g., horseradish peroxidase, beta-galactosidase, alkaline phosphataseand glucose oxidase) may generally be detected by the addition ofsubstrate (generally for a specific period of time), followed byspectroscopic or other analysis of the reaction products. Regardless ofthe specific method employed, a level of bound detection reagent that isat least two fold greater than background (i.e., the level observed fora biological sample obtained from a disease-free individual) indicatesthe presence of a malignant disease associated with WT1 expression.

In general, methods for monitoring the effectiveness of an immunizationor therapy involve monitoring changes in the level of antibodies or Tcells specific for WT1 in the patient. Methods in which antibody levelsare monitored may comprise the steps of: (a) incubating a firstbiological sample, obtained from a patient prior to a therapy orimmunization, with a WT1 polypeptide, wherein the incubation isperformed under conditions and for a time sufficient to allowimmunocomplexes to form; (b) detecting immunocomplexes formed betweenthe WT1 polypeptide and antibodies in the biological sample thatspecifically bind to the WT1 polypeptide; (c) repeating steps (a) and(b) using a second biological sample taken from the patient followingtherapy or immunization; and (d) comparing the number of immunocomplexesdetected in the first and second biological samples. Alternatively, apolynucleotide encoding a WT1 polypeptide, or an APC expressing a WT1polypeptide may be employed in place of the WT1 polypeptide. Within suchmethods, immunocomplexes between the WT1 polypeptide encoded by thepolynucleotide, or expressed by the APC, and antibodies in thebiological sample are detected.

Methods in which T cell activation and/or the number of WT1 specificprecursors are monitored may comprise the steps of: (a) incubating afirst biological sample comprising CD4+ and/or CD8+ cells (e.g., bonemarrow, peripheral blood or a fraction thereof), obtained from a patientprior to a therapy or immunization, with a WT1 polypeptide, wherein theincubation is performed under conditions and for a time sufficient toallow specific activation, proliferation and/or lysis of T cells; (b)detecting an amount of activation, proliferation and/or lysis of the Tcells; (c) repeating steps (a) and (b) using a second biological samplecomprising CD4+ and/or CD8+ T cells, and taken from the same patientfollowing therapy or immunization; and (d) comparing the amount ofactivation, proliferation and/or lysis of T cells in the first andsecond biological samples. Alternatively, a polynucleotide encoding aWT1 polypeptide, or an APC expressing a WT1 polypeptide may be employedin place of the WT1 polypeptide.

A biological sample for use within such methods may be any sampleobtained from a patient that would be expected to contain antibodies,CD4+ T cells and/or CD8+ T cells. Suitable biological samples includeblood, sera, ascites, bone marrow, pleural effusion and cerebrospinalfluid. A first biological sample may be obtained prior to initiation oftherapy or immunization or part way through a therapy or vaccinationregime. The second biological sample should be obtained in a similarmanner, but at a time following additional therapy or immunization. Thesecond biological sample may be obtained at the completion of, or partway through, therapy or immunization, provided that at least a portionof therapy or immunization takes place between the isolation of thefirst and second biological samples.

Incubation and detection steps for both samples may generally beperformed as described above. A statistically significant increase inthe number of immunocomplexes in the second sample relative to the firstsample reflects successful therapy or immunization.

The following Examples are offered by way of illustration and not by wayof limitation.

EXAMPLES Example 1 Identification of an Immune Response to WT 1 inPatients with Hematological Malignancies

This Example illustrates the identification of an existent immuneresponse in patients with a hematological malignancy.

To evaluate the presence of preexisting WT1 specific antibody responsesin patients, sera of patients with acute myelogenous leukemia (AML),acute lymphocytic leukemia (ALL), chronic myelogenous leukemia (CML) andsevere aplastic anemia were analyzed using Western blot analysis. Serawere tested for the ability to immunoprecipitate WT1 from the humanleukemic cell line K562 (American Type Culture Collection, Manassas,Va.). In each case, immunoprecipitates were separated by gelelectrophoresis, transferred to membrane and probed with the anti WT-1antibody WT180 (Santa Cruz Biotechnology, Inc., Santa Cruz, Calif.).This Western blot analysis identified potential WT1 specific antibodiesin patients with hematological malignancy. A representative Western blotshowing the results for a patient with AML is shown in FIG. 2. A 52 kDprotein in the immunoprecipitate generated using the patient sera wasrecognized by the WT1 specific antibody. The 52 kD protein migrated atthe same size as the positive control.

Additional studies analyzed the sera of patients with AML and CML forthe presence of antibodies to full-length and truncated WT1 proteins.CDNA constructs representing the human WT1/full-length (aa 1–449), theN-terminus (aa 1–249) (WT1/N-terminus) and C-terminuis (aa 267–449)(WT1/C-terminus) region were subcloned into modified pET28 vectors. TheWT1/full-length and WT1/N-terminus proteins were expressed as Ra12fusion proteins. Ra12 is the C-terminal fragment of a secretedMycobacterium tuberculosis protein, denoted as MTB32B. (Skeiky et al.,Infect Immun. 67;3998, 1999). The Ra12-WT1/full-length fusion region wascloned 3′ to a histidine-tag in a histidine-tag modified pET28 vector.The WT1/N-terminus region was subcloned into a modified pET28 vectorthat has a 5′ histidine-tag followed by the thioredoxin(TRX)-WT1/N-terminus fusion region followed by a 3′ histidine-tag. TheWT1/C-terminus coding region was subcloned into a modified pET28 vectorwithout a fusion partner containing only the 5′ and 3′ histidine-tag,followed by a Thrombin and EK site.

BL21 pLysS E. coli (Stratagene, La Jolla, Calif.) were transformed withthe three WT1 expression constructs, grown overnight and induced withisopropyl-β-D-thiogalactoside (IPTG). WT1 proteins were purified asfollows: Cells were harvested and lysed by incubation in 10 mM Tris, pH8.0 with Complete Protease Inhibitor Tablets (Boehringer MannheimBiochemicals, Indianapolis, Ind.) at 37° C. followed by repeated roundsof sonication. Inclusion bodies were washed twice with 10 mM Tris, pH8.0. Proteins were then purified by metal chelate affinitychromatography over nickel-nitrilotriacetic acid resin (QIAGEN Inc.,Valencia, Calif.; Hochuli et al., Biologically Active Molecules:217,1989) followed by chromatography on a Source Q anion exchange resin(Amersham Pharmacia Biotech, Upsala, Sweden). The identity of the WT1proteins was confirmed by N-terminal sequencing.

Sera from adult patients with de nova AML or CML were studied for thepresence of WT1 specific Ab. Recombinant proteins were adsorbed to TCmicrowell plates (Nunc, Roskilde, Denmark). Plates were washed withPBS/0.5% Tween 20 and blocked with 1% BSA/PBS/0.1% Tween 20. Afterwashing, serum dilutions were added and incubated overnight at 4° C.Plates were washed and Donkey anti-human IgG-HRP secondary antibody wasadded (Jackson-Immunochem, West Grove, Pa.) and incubated for 2 h atroom temperature. Plates were washed, incubated with TMB Peroxidasesubstrate solution (Kirkegaard and Perry Laboratories, MA), quenchedwith 1N H₂SO₄, and immediately read (Cyto-Fluor 2350; Millipore,Bedford, Mass.).

For the serological survey, human sera were tested by ELISA over a rangeof serial dilutions from 1:50 to 1:20,000. A positive reaction wasdefined as an OD value of a 1:500 diluted serum that exceeded the meanOD value of sera from normal donors (n=96) by three (WT1/full-length,WT1C-terminus) standard deviations. Due to a higher background in normaldonors to the WT1/N-terminus protein a positive reaction toWT1/N-terminus was defined as an OD value of 1:500 diluted serum thatexceeded the mean OD value of sera from normal donors by four standarddeviations. To verify that the patient Ab response was directed againstWT1 and not to the Ra12 or TRX fusion part of the protein or possible E.coli contaminant proteins, controls included the Ra12 and TRX proteinalone purified in a similar manner. Samples that showed reactivityagainst the Ra12 and/or TRX proteins were excluded from the analysis.

To evaluate for the presence of immunity to WT1, Ab to recombinantfull-length and truncated WT1 proteins in the sera of normal individualsand patients with leukemia were detected. Antibody reactivity wasdetermined by ELISA reactivity to WT1/full-length protein,WT1/N-terminus protein and WT1/C-terminus protein. A positive reactionwas defined as an OD value of a 1:500 diluted serum that exceeded themean OD value of all sera from normal donors (n=96) by either threestandard deviations (WT1/full-length protein and WT1/C-terminus protein)or four standard deviations (WT1/N-terminus protein). The ELISA forWT1/C-terminus protein had a higher background in normal individuals andleukemia patients. Thus, the cut off was set a level higher.

Only 2 of 96 normal donors had serum antibodies reactive withWT1/full-length protein (FIG. 18). One of those individuals had antibodyto WT1/N-terminus protein and one had antibody to WT1/C-terminusprotein. In contrast, 14 of 63 patients (22%) with AML had serumantibodies reactive with WT1/full-length protein (FIG. 19). Similarly,16 of 63 patients (25%) had serum antibodies reactive withWT1/N-terminus (FIG. 14). Serum from all of the 14 patients withreactivity to WT1/full-length also reacted with WT1/N-terminus protein.Two additional patients had reactivity to only WT1/N-terminus protein.By marked contrast, only 2 of 63 patients (3%) had reactivity toWT1/C-terminus protein. 15 of 81 patients (19%) with CML had serumantibodies reactive with WT1/full-length protein and 12 of 81 patients(15%) had serum antibodies reactive with WT1/N-terminus. Only 3 of 81patients (3%) had reactivity to WT1/C-terminus protein. (FIGS. 16 and17.)

These data demonstrate that Ab responses to WT1 are detectable in somepatients with AML and CML. The greater incidence of antibody in leukemiapatients provides strong evidence that immunization to the WT1 proteinoccurred as a result of patients bearing malignancy that expresses or atsome time expressed WT1. Without being limited to a specific theory, itis believed that the observed antibody responses to WT1 most probablyresult from patients becoming immune to WT1 on their own leukemia cellsand provide direct evidence that WT1 can be immunogenic despite being a“self” protein.

The presence of antibody to WT1 strongly implies that concurrent helperT cell responses are also present in the same patients. WT1 is aninternal protein. Thus, CTL responses are likely to be the mosteffective in terms of leukemia therapy and the most toxic arm ofimmunity. Thus, these data provide evidence that therapeutic vaccinesdirected against WT1 will be able to elicit an immune response to WT1.

The majority of the antibodies detected were reactive with epitopeswithin the N-terminus while only a small subgroup of patients showed aweak antibody response to the C-terminus. This is consistent withobservations in the animal model, where immunization with peptidesderived from the N-terminus elicited antibody, helper T cell and CTLresponses, whereas none of the peptides tested from the C-terminuselicited antibody or T cell responses (Gaiger et al., Blood 96:1334,2000).

Example 2 Induction of Antibodies to WT1 in Mice Immunized with CellLines Expressing WT1

This Example illustrates the use of cells expressing WT1 to induce a WT1specific antibody response in vivo.

Detection of existent antibodies to WT1 in patients with leukemiastrongly implied that it is possible to immunize to WT1 protein toelicit immunity to WT1. To test whether immunity to WT1 can be generatedby vaccination, mice were injected with TRAMP-C, a WT1 positive tumorcell line of B6 origin. Briefly, male B6 mice were immunized with 5×10⁶TRAMP-C cells subcutaneously and boosted twice with 5×10⁶ cells at threeweek intervals. Three weeks after the final immunization, sera wereobtained and single cell suspensions of spleens were prepared in RPMI1640 medium (GIBCO) with 25 μM β-2-mercaptoethanol, 200 units ofpenicillin per ml, 10 mM L-glutamine, and 10% fetal bovine serum.

Following immunization to TRAMP-C, a WT1 specific antibody response inthe immunized animals was detectable. A representative Western blot isshown in FIG. 3. These results show that immunization to WT1 protein canelicit an immune response to WT1 protein.

Example 3 Induction of Th and Antibody Responses in Mice Immunized withWT1 Peptides

This Example illustrates the ability of immunization with WT1 peptidesto elicit an immune response specific for WT1.

Peptides suitable for eliciting Ab and proliferative T cell responseswere identified according to the Tsites program (Rothbard and Taylor,EMBO J. 7:93–100, 1988; Deavin et al., Mol. Immunol. 33:145–155, 1996),which searches for peptide motifs that have the potential to elicit Thresponses. Peptides shown in Table I were synthesized and sequenced.

TABLE I WT1 Peptides Peptide Sequence Comments Mouse: p6–22RDLNALLPAVSSLGGGG 1 mismatch (SEQ ID NO:13) relative to human WT1sequence Human: p6–22 RDLNALLPAVPSLGGGG (SEQ ID NO:1) Human/mouse:PSQASSGQARMFPNAPYLPSCLE p117–139 (SEQ ID NOs:2 and 3) Mouse: p244–262GATLKGMAAGSSSSVKWTE 1 mismatch (SEQ ID NO:14) relative to human WT1sequence Human: GATLKGVAAGSSSSVKWTE p244–262 (SEQ ID NO:4) Human/mouse:RIHTHGVFRGIQDVR p287–301 (SEQ ID NOs:15 and 16) Mouse: p299–313VRRVSGVAPTLVRS 1 mismatch (SEQ ID NO:17) relative to human WT1 sequenceHuman/mouse: CQKKFARSDELVRHH p421–435 (SEQ ID NOs:19 and 20)

For immunization, peptides were grouped as follows:

Group A:

-   -   p6–22 human: 10.9 mg in 1 ml (10 μl=100 μg)    -   p117–139 human/mouse: 7.6 mg in 1 ml (14 μl=100 μg)    -   p244–262 human: 4.6 mg in 1 ml (221 μl=100 μg)

Group B:

-   -   p287–301 human/mouse: 7.2 mg in 1 ml (14 μl=100 μg)    -   mouse p299–313: 6.6 mg in 1 ml (15 μl=100 μg)    -   p421–435 human/mouse: 3.3 mg in 1 ml (30 μl=100 μg)

Control:

-   -   (FBL peptide 100 μg)+CFA/IFA

Control:

-   -   (CD45 peptide 100 μg)+CFA/IFA

Group A contained peptides present within the amino terminus portion ofWT1 (exon 1) and Group B contained peptides present within the carboxyterminus, which contains a four zinc finger region with sequencehomology to other DNA-binding proteins. Within group B, p287–301 andp299–313 were derived from exon 7, zinc finger 1, and p421–435 wasderived from exon 10, zinc finger IV.

B6 mice were immunized with a group of WT1 peptides or with a controlpeptide. Peptides were dissolved in 1 ml sterile water for injection,and B6 mice were immunized 3 times at time intervals of three weeks.Adjuvants used were CFA/IFA, GM-CSF, and Montinide. The presence ofantibodies specific for WT1 was then determined as described in Examples1 and 2, and proliferative T cell responses were evaluated using astandard thymidine incorporation assay, in which cells were cultured inthe presence of antigen and proliferation was evaluated by measuringincorporated radioactivity (Chen et al., Cancer Res. 54:1065–1070,1994). In particular, lymphocytes were cultured in 96-well plates at2×10⁵ cells per well with 4×10⁵ irradiated (3000 rads) syngeneic spleencells and the designated peptide.

Immunization of mice with the group of peptides designated as Group Aelicited an antibody response to WT1 (FIG. 4). No antibodies weredetected following immunization to Vaccine B, which is consistent with alack of helper T cell response from immunization with Vaccine B.P117–139 elicited proliferative T cell responses (FIGS. 5A–5C). Thestimulation indices (SI) varied between 8 and 72. Other peptides (P6–22and P299–313) also were shown to elicit proliferative T cell responses.Immunization with P6–22 resulted in a stimulation index (SI) of 2.3 andimmunization with P299–313 resulted in a SI of 3.3. Positive controlsincluded ConA stimulated T cells, as well as T cells stimulated withknown antigens, such as CD45 and FBL, and allogeneic T cell lines(DeBruijn et al., Eur. J. Immunol. 21:2963–2970, 1991).

FIGS. 6A and 6B show the proliferative response observed for each of thethree peptides within vaccine A (FIG. 6A) and vaccine B (FIG. 6B).Vaccine A elicited proliferative T cell responses to the immunizingpeptides p6–22 and p117–139, with stimulation indices (SI) varyingbetween 3 and 8 (bulk lines). No proliferative response to p244–262 wasdetected (FIG. 6A).

Subsequent in vitro stimulations were carried out as single peptidestimulations using only p6–22 and p117–139. Stimulation of the Vaccine Aspecific T cell line with p117–139 resulted in proliferation to p117–139with no response to p6–22 (FIG. 7A). Clones derived from the line werespecific for p117–139 (FIG. 7B). By contrast, stimulation of the VaccineA specific T cell line with p6–22 resulted in proliferation to p6–22with no response to p117–139 (FIG. 7C). Clones derived from the linewere specific for p6–22 (FIG. 7D).

These results show that vaccination with WT1 peptides can elicitantibody responses to WT1 protein and proliferative T cell responses tothe immunizing peptides.

Example 4 Induction of CTL Responses in Mice Immunized with WT1 Peptides

This Example illustrates the ability of WT1 peptides to elicit CTLimmunity.

Peptides (9-mers) with motifs appropriate for binding to class I MHCwere identified using a BIMAS HLA peptide binding prediction analysis(Parker et al., J. Immunol. 152:163, 1994). Peptides identified withinsuch analyses are shown in Tables II–XLIV. In each of these tables, thescore reflects the theoretical binding affinity (half-time ofdissociation) of the peptide to the MHC molecule indicated.

Peptides identified using the Tsites program (Rothbard and Taylor, EMBOJ. 7:93–100, 1988; Deavin et al., Mol. Immunol. 33:145–155, 1996), whichsearches for peptide motifs that have the potential to elicit Thresponses are further shown in FIGS. 8A and 8B, and Table XLV.

TABLE II Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A1 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 137 CLESQPAIR 18.000(SEQ ID NO:47)  2 80 GAEPHEEQC 9.000 (SEQ ID NO:87)  3 40 FAPPGASAY5.000 (SEQ ID NO:74)  4 354 QCDFKDCER 5.000 (SEQ ID NO:162) 5 2GSDVRDLNA 3.750 (SEQ ID NO:101) 6 152 VTFDGTPSY 2.500 (SEQ ID NO:244) 7260 WTEGQSNHS 2.250 (SEQ ID NO:247) 8 409 TSEKPFSCR 1.350 (SEQ IDNO:232) 9 73 KQEPSWGGA 1.350 (SEQ ID NO:125) 10 386 KTCQRKFSR 1.250 (SEQID NO:128) 11 37 VLDFAPPGA 1.000 (SEQ ID NO:241) 12 325 CAYPGCNKR 1.000(SEQ ID NO:44)  13 232 QLECMTWNQ 0.900 (SEQ ID NO:167) 14 272 ESDNHTTPI0.750 (SEQ ID NO:71)  15 366 RSDQLKRHQ 0.750 (SEQ ID NO:193) 16 222SSDNLYQMT 0.750 (SEQ ID NO:217) 17 427 RSDELVRHH 0.750 (SEQ ID NO:191)18 394 RSDHLKTHT 0.750 (SEQ ID NO:192) 19 317 TSEKRPFMC 0.675 (SEQ IDNO:233) 20 213 QALLLRTPY 0.500 (SEQ ID NO:160)

TABLE III Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A 0201 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 126 RMFPNAPYL 313.968(SEQ ID NO:185) 2 187 SLGEQQYSV 285.163 (SEQ ID NO:214) 3 10 ALLPAVPSL181.794 (SEQ ID NO:34)  4 242 NLGATLKGV 159.970 (SEQ ID NO:146) 5 225NLYQMTSQL 68.360 (SEQ ID NO:147) 6 292 GVFRGIQDV 51.790 (SEQ ID NO:103)7 191 QQYSVPPPV 22.566 (SEQ ID NO:171) 8 280 ILCGAQYRI 17.736 (SEQ IDNO:116) 9 235 CMTWNQMNL 15.428 (SEQ ID NO:49)  10 441 NMTKLQLAL 15.428(SEQ ID NO:149) 11 7 DLNALLPAV 11.998 (SEQ ID NO:58)  12 227 YQMTSQLEC8.573 (SEQ ID NO:251) 13 239 NQMNLGATL 8.014 (SEQ ID NO:151) 14 309TLVRSASET 7.452 (SEQ ID NO:226) 15 408 KTSEKPFSC 5.743 (SEQ ID NO:129)16 340 LQMHSRKHT 4.752 (SEQ ID NO:139) 17 228 QMTSQLECM 4.044 (SEQ IDNO:169) 18 93 TVHFSGQFT 3.586 (SEQ ID NO:235) 19 37 VLDFAPPGA 3.378 (SEQID NO:241) 20 86 EQCLSAFTV 3.068 (SEQ ID NO:69) 

TABLE IV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A 0205 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 10 ALLPAVPSL 42.000 (SEQID NO:34)  2 292 GVFRGIQDV 24.000 (SEQ ID NO:103) 3 126 RMFPNAPYL 21.000(SEQ ID NO:185) 4 225 NLYQMTSQL 21.000 (SEQ ID NO:147) 5 239 NQMNLGATL16.800 (SEQ ID NO:151) 6 302 RVPGVAPTL 14.000 (SEQ ID NO:195) 7 441NMTKLQLAL 7.000 (SEQ ID NO:149) 8 235 CMTWNQMNL 7.000 (SEQ ID NO:49)  9187 SLGEQQYSV 6.000 (SEQ ID NO:214) 10 191 QQYSVPPPV 4.800 (SEQ IDNO:171) 11 340 LQMHSRKHT 4.080 (SEQ ID NO:139) 12 242 NLGATLKGV 4.000(SEQ ID NO:146) 13 227 YQMTSQLEC 3.600 (SEQ ID NO:251) 14 194 SVPPPVYGC2.000 (SEQ ID NO:218) 15 93 TVHFSGQFT 2.000 (SEQ ID NO:235) 16 280ILCGAQYRI 1.700 (SEQ ID NO:116) 17 98 GQFTGTAGA 1.200 (SEQ ID NO:99)  18309 TLVRSASET 1.000 (SEQ ID NO:226) 19 81 AEPHEEQCL 0.980 (SEQ IDNO:30)  20 73 KQEPSWGGA 0.960 (SEQ ID NO:125)

TABLE V Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A24 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 302 RVPGVAPTL 16.800(SEQ ID NO:195) 2 218 RTPYSSDNL 12.000 (SEQ ID NO:194) 3 356 DFKDCERRF12.000 (SEQ ID NO:55)  4 126 RMFPNAPYL 9.600 (SEQ ID NO:185) 5 326AYPGCNKRY 7.500 (SEQ ID NO:42)  6 270 GYESDNHT 7.500   (SEQ ID NO:106)T7 239 NQMNLGATL 7.200 (SEQ ID NO:151) 8 10 ALLPAVPSL 7.200 (SEQ IDNO:34)  9 130 NAPYLPSCL 7.200 (SEQ ID NO:144) 10 329 GCNKRYFKL 6.600(SEQ ID NO:90)  11 417 RWPSCQKKF 6.600 (SEQ ID NO:196) 12 47 AYGSLGGPA6.000 (SEQ ID NO:41)  13 180 DPMGQQGSL 6.000 (SEQ ID NO:59)  14 4DVRDLNALL 5.760 (SEQ ID NO:62)  15 285 QYRIHTHGV 5.000 (SEQ ID NO:175)16 192 QYSVPPPVY 5.000 (SEQ ID NO:176) 17 207 DSCTGSQAL 4.800 (SEQ IDNO:61)  18 441 NMTKLQLAL 4.800 (SEQ ID NO:149) 19 225 NLYQMTSQL 4.000(SEQ ID NO:147) 20 235 CMTWNQMNL 4.000 (SEQ ID NO:49) 

TABLE VI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A3 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 436 NMHQRNMTK 40.000(SEQ ID NO:148) 2 240 QMNLGATLK 20.000 (SEQ ID NO:168) 3 88 CLSAFTVHF6.000 (SEQ ID NO:48)  4 126 RMFPNAPYL 4.500 (SEQ ID NO:185) 5 169AQFPNHSFK 4.500 (SEQ ID NO:36)  6 10 ALLPAVPSL 4.050 (SEQ ID NO:34)  7137 CLESQPAIR 4.000 (SEQ ID NO:47)  8 225 NLYQMTSQL 3.000 (SEQ IDNO:147) 9 32 AQWAPVLDF 2.700 (SEQ ID NO:37)  10 280 ILCGAQYRI 2.700 (SEQID NO:116) 11 386 KTCQRKFSR 1.800 (SEQ ID NO:128) 12 235 CMTWNQMNL 1.200(SEQ ID NO:49)  13 441 NMTKLQLAL 1.200 (SEQ ID NO:149) 14 152 VTFDGTPSY1.000 (SEQ ID NO:244) 15 187 SLGEQQYSV 0.900 (SEQ ID NO:214) 16 383FQCKTCQRK 0.600 (SEQ ID NO:80)  17 292 GVFRGIQDV 0.450 (SEQ ID NO:103)18 194 SVPPPVYGC 0.405 (SEQ ID NO:218) 19 287 RIHTHGVFR 0.400 (SEQ IDNO:182) 20 263 GQSNHSTGY 0.360 (SEQ ID NO:100)

TABLE VII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A68.1 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 100 FTGTAGACR 100.000(SEQ ID NO:84)  2 386 KTCQRKFSR 50.000 (SEQ ID NO:128) 3 368 DQLKRHQRR30.000 (SEQ ID NO:60)  4 312 RSASETSEK 18.000 (SEQ ID NO:190) 5 337LSHLQMHSR 15.000 (SEQ ID NO:141) 6 364 FSRSDQLKR 15.000 (SEQ ID NO:83) 7 409 TSEKPFSCR 15.000 (SEQ ID NO:232) 8 299 DVRRVPGVA 12.000 (SEQ IDNO:63)  9 4 DVRDLNALL 12.000 (SEQ ID NO:62)  10 118 SQASSGQAR 10.000(SEQ ID NO:216) 11 343 HSRKHTGEK 9.000 (SEQ ID NO:111) 12 169 AQFPNHSFK9.000 (SEQ ID NO:36)  13 292 GVFRGIQDV 8.000 (SEQ ID NO:103) 14 325CAYPGCNKR 7.500 (SEQ ID NO:44)  15 425 FARSDELVR 7.500 (SEQ ID NO:75) 16 354 QCDFKDCER 7.500 (SEQ ID NO:162) 17 324 MCAYPGCNK 6.000 (SEQ IDNO:142) 18 251 AAGSSSSVK 6.000 (SEQ ID NO:28)  19 379 GVKPFQCKT 6.000(SEQ ID NO:104) 20 137 CLESQPAIR 5.000 (SEQ ID NO:47) 

TABLE VIII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A 1101 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 386 KTCQRKFSR 1.800 (SEQID NO:128) 2 169 AQFPNHSFK 1.200 (SEQ ID NO:36)  3 436 NMHQRNMTK 0.800(SEQ ID NO:148) 4 391 KFSRSDHLK 0.600 (SEQ ID NO:120) 5 373 HQRRHTGVK0.600 (SEQ ID NO:109) 6 383 FQCKTCQRK 0.600 (SEQ ID NO:80)  7 363RFSRSDQLK 0.600 (SEQ ID NO:178) 8 240 QMNLGATLK 0.400 (SEQ ID NO:168) 9287 RIHTHGVFR 0.240 (SEQ ID NO:182) 10 100 FTGTAGACR 0.200 (SEQ IDNO:84)  11 324 MCAYPGCNK 0.200 (SEQ ID NO:142) 12 251 AAGSSSSVK 0.200(SEQ ID NO:28)  13 415 SCRWPSCQK 0.200 (SEQ ID NO:201) 14 118 SQASSGQAR0.120 (SEQ ID NO:216) 15 292 GVFRGIQDV 0.120 (SEQ ID NO:103) 16 137CLESQPAIR 0.080 (SEQ ID NO:47)  17 425 FARSDELVR 0.080 (SEQ ID NO:75) 18 325 CAYPGCNKR 0.080 (SEQ ID NO:44)  19 312 RSASETSEK 0.060 (SEQ IDNO:190) 20 65 PPPPHSFI 0.060   (SEQ ID NO:156)K

TABLE IX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A 3101 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 386 KTCQRKFSR 9.000 (SEQID NO:128) 2 287 RIHTHGVFR 6.000 (SEQ ID NO:182) 3 137 CLESQPAIR 2.000(SEQ ID NO:47)  4 118 SQASSGQAR 2.000 (SEQ ID NO:216) 5 368 DQLKRHQRR1.200 (SEQ ID NO:60)  6 100 FTGTAGACR 1.000 (SEQ ID NO:84)  7 293VFRGIQDVR 0.600 (SEQ ID NO:238) 8 325 CAYPGCNKR 0.600 (SEQ ID NO:44)  9169 AQFPNHSFK 0.600 (SEQ ID NO:36)  10 279 PILCGAQYR 0.400 (SEQ IDNO:155) 11 436 NMHQRNMTK 0.400 (SEQ ID NO:148) 12 425 FARSDELVR 0.400(SEQ ID NO:75)  13 32 AQWAPVLDF 0.240 (SEQ ID NO:37)  14 240 QMNLGATLK0.200 (SEQ ID NO:168) 15 354 QCDFKDCER 0.200 (SEQ ID NO:162) 16 373HQRRHTGVK 0.200 (SEQ ID NO:109) 17 383 FQCKTCQRK 0.200 (SEQ ID NO:80) 18 313 SASETSEKR 0.200 (SEQ ID NO:197) 19 358 KDCERRFSR 0.180 (SEQ IDNO:118) 20 391 KFSRSDHLK 0.180 (SEQ ID NO:120)

TABLE X Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA A 3302 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 337 LSHLQMHSR (SEQ15.000 ID NO:141) 2 409 TSEKPFSCR (SEQ ID 15.000 NO:232) 3 364 FSRSDQLKR(SEQ ID 15.000 NO:83) 4 137 CLESQPAIR (SEQ ID 9.000 NO:47) 5 368DQLKRHQRR (SEQ 9.000 ID NO:60) 6 287 RIHTHGVFR (SEQ ID 4.500 NO:182) 7210 TGSQALLLR (SEQ ID 3.000 NO:223) 8 425 FARSDELVR (SEQ 3.000 ID NO:75)9 313 SASETSEKR (SEQ ID 3.000 NO:197) 10 293 VFRGIQDVR (SEQ ID 3.000NO:238) 11 354 QCDFKDCER (SEQ 3.000 ID NO:162) 12 100 FTGTAGACR (SEQ3.000 ID NO:84) 13 118 SQASSGQAR(SEQ 3.000 ID NO:216) 14 325 CAYPGCNKR(SEQ 3.000 ID NO:44) 15 207 DSCTGSQAL (SEQ 1.500 ID NO:61) 16 139ESQPAIRNQ (SEQ ID 1.500 NO:72) 17 299 DVRRVPGVA (SEQ 1.500 ID NO:63) 18419 PSCQKKFAR (SEQ 1.500 ID NO:159) 19 272 ESDNHTTPI (SEQ ID 1.500NO:71) 20 4 DVRDLNALL (SEQ 1.500 ID NO:62)

TABLE XI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B14 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 362 RRFSRSDQL (SEQ ID1000.000 NO:187) 2 332 KRYFKLSHL (SEQ 300.000 ID NO:127) 3 423 KKFARSDEL(SEQ 150.000 ID NO:122) 4 390 RKFSRSDHL (SEQ ID 150.000 NO:183) 5 439QRNMTKLQL (SEQ 20.000 ID NO:173) 6 329 GCNKRYFKL (SEQ 10.000 ID NO:90) 710 ALLPAVPSL (SEQ ID 10.000 NO:34) 8 180 DPMGQQGSL (SEQ 9.000 ID NO:59)9 301 RRVPGVAPT (SEQ 6.000 ID NO:189) 10 126 RMFPNAPYL (SEQ 5.000 IDNO:185) 11 371 KRHQRRHTG (SEQ 5.000 ID NO:126) 12 225 NLYQMTSQL (SEQ5.000 ID NO:147) 13 144 IRNQGYSTV (SEQ ID 4.000 NO:117) 14 429 DELVRHHNM(SEQ 3.000 ID NO:53) 15 437 MHQRNMTKL (SEQ 3.000 ID NO:143) 16 125ARMFPNAPY (SEQ 3.000 ID NO:38) 17 239 NQMNLGATL (SEQ 3.000 ID NO:151) 18286 YRIHTHGVF (SEQ ID 3.000 NO:252) 19 174 HSFKHEDPM (SEQ 3.000 IDNO:110) 20 372 RHQRRHTGV (SEQ 3.000 ID NO:181)

TABLE XII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B40 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 81 AEPHEEQCL (SEQ ID40.000 NO:30) 2 429 DELVRHHNM (SEQ 24.000 ID NO:53) 3 410 SEKPFSCRW (SEQ20.000 ID NO:207) 4 318 SEKRPFMCA (SEQ 15.000 ID NO:208) 5 233 LECMTWNQM(SEQ 12.000 ID NO:131) 6 3 SDVRDLNAL (SEQ 10.000 ID NO:206) 7 349GEKPYQCDF (SEQ 8.000 ID NO:91) 8 6 RDLNALLPA (SEQ 5.000 ID NO:177) 9 85EEQCLSAFT (SEQ ID 4.000 NO:65) 10 315 SETSEKRPF (SEQ ID 4.000 NO:209) 11261 TEGQSNHST (SEQ ID 4.000 NO:221) 12 23 GCALPVSGA (SEQ 3.000 ID NO:89)13 38 LDFAPPGAS (SEQ ID 3.000 NO:130) 14 273 SDNHTTPIL (SEQ ID 2.500NO:204) 15 206 TDSCTGSQA (SEQ 2.500 ID NO:220) 16 24 CALPVSGAA (SEQ2.000 ID NO:43) 17 98 GQFTGTAGA (SEQ 2.000 ID NO:99) 18 30 GAAQWAPVL(SEQ 2.000 ID NO:86) 19 84 HEEQCLSAF (SEQ ID 2.000 NO:107) 20 26LPVSGAAQW (SEQ 2.000 ID NO:138)

TABLE XIII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B60 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 81 AEPHEEQCL (SEQ ID160.000 NO:30) 2 3 SDVRDLNAL (SEQ 40.000 ID NO:206) 3 429 DELVRHHNM (SEQ40.000 ID NO:53) 4 233 LECMTWNQM (SEQ 22.000 ID NO:131) 5 273 SDNHTTPIL(SEQ ID 20.000 NO:204) 6 209 CTGSQALLL (SEQ ID 8.000 NO:52) 7 30GAAQWAPVL (SEQ 8.000 ID NO:86) 8 318 SEKRPFMCA (SEQ 8.000 ID NO:208) 9180 DPMGQQGSL (SEQ 8.000 ID NO:59) 10 138 LESQPAIRN (SEQ ID 5.280NO:132) 11 239 NQMNLGATL (SEQ 4.400 ID NO:151) 12 329 GCNKRYFKL (SEQ4.400 ID NO:90) 13 130 NAPYLPSCL (SEQ ID 4.400 NO:144) 14 85 EEQCLSAFT(SEQ ID 4.400 NO:65) 15 208 SCTGSQALL (SEQ ID 4.000 NO:202) 16 207DSCTGSQAL (SEQ 4.000 ID NO:61) 17 218 RTPYSSDNL (SEQ ID 4.000 NO:194) 18261 TEGQSNHST (SEQ ID 4.000 NO:221) 19 18 LGGGGGCAL (SEQ 4.000 IDNO:134) 20 221 YSSDNLYQM (SEQ 2.200 ID NO:253)

TABLE XIV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B61 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 318 SEKRPFMCA (SEQ20.000 ID NO:208) 2 429 DELVRHHNM (SEQ 16.000 ID NO:53) 3 298 QDVRRVPGV(SEQ 10.000 ID NO:164) 4 81 AEPHEEQCL (SEQ ID 8.000 NO:30) 5 233LECMTWNQM (SEQ 8.000 ID NO:131) 6 6 RDLNALLPA (SEQ 5.500 ID NO:177) 7 85EEQCLSAFT (SEQ ID 4.000 NO:65) 8 261 TEGQSNHST (SEQ ID 4.000 NO:221) 9206 TDSCTGSQA (SEQ 2.500 ID NO:220) 10 295 RGIQDVRRV (SEQ 2.200 IDNO:179) 11 3 SDVRDLNAL (SEQ 2.000 ID NO:206) 12 250 VAAGSSSSV (SEQ 2.000ID NO:236) 13 29 SGAAQWAPV (SEQ 2.000 ID NO:211) 14 315 SETSEKRPF (SEQID 1.600 NO:209) 15 138 LESQPAIRN (SEQ ID 1.200 NO:132) 16 244 GATLKGVAA(SEQ 1.100 ID NO:88) 17 20 GGGGCALPV (SEQ 1.100 ID NO:92) 18 440RNMTKLQLA (SEQ 1.100 ID NO:186) 19 23 GCALPVSGA (SEQ 1.100 ID NO:89) 20191 QQYSVPPPV (SEQ 1.000 ID NO:171)

TABLE XV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B62 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 146 NQGYSTVTF (SEQ211.200 ID NO:150) 2 32 AQWAPVLDF (SEQ 96.000 ID NO:37) 3 263 GQSNHSTGY(SEQ 96.000 ID NO:100) 4 88 CLSAFTVHF (SEQ ID 96.000 NO:48) 5 17SLGGGGGCA (SEQ 9.600 ID NO:215) 6 239 NQMNLGATL (SEQ 8.800 ID NO:151) 7191 QQYSVPPPV (SEQ 8.000 ID NO:171) 8 98 GQFTGTAGA (SEQ 8.000 ID NO:99)9 384 QCKTCQRKF (SEQ 6.000 ID NO:163) 10 40 FAPPGASAY (SEQ 4.800 IDNO:74) 11 227 YQMTSQLEC (SEQ 4.800 ID NO:251) 12 187 SLGEQQYSV (SEQ4.400 ID NO:214) 13 86 EQCLSAFTV (SEQ ID 4.400 NO:69) 14 152 VTFDGTPSY(SEQ ID 4.400 NO:244) 15 101 TGTAGACRY (SEQ 4.000 ID NO:224) 16 242NLGATLKGV (SEQ 4.000 ID NO:146) 17 92 FTVHFSGQF (SEQ ID 4.000 NO:85) 187 DLNALLPAV (SEQ 4.000 ID NO:58) 19 123 GQARMFPNA (SEQ 4.000 ID NO:98)20 280 ILCGAQYRI (SEQ ID 3.120 NO:116)

TABLE XVI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B7 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 180 DPMGQQGSL (SEQ240.000 ID NO:59) 2 4 DVRDLNALL (SEQ 200.000 ID NO:62) 3 302 RVPGVAPTL(SEQ 20.000 ID NO:195) 4 30 GAAQWAPVL (SEQ 12.000 ID NO:86) 5 239NQMNLGATL (SEQ 12.000 ID NO:151) 6 130 NAPYLPSCL (SEQ ID 12.000 NO:144)7 10 ALLPAVPSL (SEQ ID 12.000 NO:34) 8 299 DVRRVPGVA (SEQ 5.000 IDNO:63) 9 208 SCTGSQALL (SEQ ID 4.000 NO:202) 10 303 VPGVAPTLV (SEQ 4.000ID NO:242) 11 18 LGGGGGCAL (SEQ 4.000 ID NO:134) 12 218 RTPYSSDNL (SEQID 4.000 NO:194) 13 207 DSCTGSQAL (SEQ 4.000 ID NO:61) 14 209 CTGSQALLL(SEQ ID 4.000 NO:52) 15 329 GCNKRYFKL (SEQ 4.000 ID NO:90) 16 235CMTWNQMNL (SEQ 4.000 ID NO:49) 17 441 NMTKLQLAL (SEQ 4.000 ID NO:149) 18126 RMFPNAPYL (SEQ 4.000 ID NO:185) 19 225 NLYQMTSQL (SEQ 4.000 IDNO:147) 20 143 AIRNQGYST (SEQ ID 3.000 NO:33)

TABLE XVII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B8 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 329 GCNKRYFKL (SEQ16.000 ID NO:90) 2 4 DVRDLNALL (SEQ 12.000 ID NO:62) 3 316 ETSEKRPFM(SEQ ID 3.000 NO:73) 4 180 DPMGQQGSL (SEQ 1.600 ID NO:59) 5 208SCTGSQALL (SEQ ID 0.800 NO:202) 6 130 NAPYLPSCL (SEQ ID 0.800 NO:144) 7244 GATLKGVAA (SEQ 0.800 ID NO:88) 8 30 GAAQWAPVL (SEQ 0.800 ID NO:86) 9299 DVRRVPGVA (SEQ 0.400 ID NO:63) 10 420 SCQKKFARS (SEQ 0.400 IDNO:200) 11 387 TCQRKFSRS (SEQ ID 0.400 NO:219) 12 225 NLYQMTSQL (SEQ0.400 ID NO:147) 13 141 QPAIRNQGY (SEQ 0.400 ID NO:170) 14 10 ALLPAVPSL(SEQ ID 0.400 NO:34) 15 207 DSCTGSQAL (SEQ 0.400 ID NO:61) 16 384QCKTCQRKF (SEQ 0.400 ID NO:163) 17 136 SCLESQPAI (SEQ ID 0.300 NO:198)18 347 HTGEKPYQC (SEQ 0.300 ID NO:112) 19 401 HTRTHTGKT (SEQ 0.200 IDNO:114) 20 332 KRYFKLSHL (SEQ 0.200 ID NO:127)

TABLE XVIII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 2702 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 332 KRYFKLSHL (SEQ900.000 ID NO:127) 2 362 RRFSRSDQL (SEQ ID 900.000 NO:187) 3 286YRIHTHGVF (SEQ ID 200.000 NO:252) 4 125 ARMFPNAPY (SEQ 200.000 ID NO:38)5 375 RRHTGVKPF (SEQ 180.000 ID NO:188) 6 32 AQWAPVLDF (SEQ 100.000 IDNO:37) 7 301 RRVPGVAPT (SEQ 60.000 ID NO:189) 8 439 QRNMTKLQL (SEQ60.000 ID NO:173) 9 126 RMFPNAPYL (SEQ 22.500 ID NO:185) 10 426ARSDELVRH (SEQ 20.000 ID NO:39) 11 146 NQGYSTVTF (SEQ 20.000 ID NO:150)12 144 IRNQGYSTV (SEQ ID 20.000 NO:117) 13 389 QRKFSRSDH (SEQ 20.000 IDNO:172) 14 263 GQSNHSTGY (SEQ 20.000 ID NO:100) 15 416 CRWPSCQKK (SEQ20.000 ID NO:50) 16 191 QQYSVPPPV (SEQ 10.000 ID NO:171) 17 217LRTPYSSDN (SEQ ID 10.000 NO:140) 18 107 CRYGPFGPP (SEQ ID 10.000 NO:51)19 98 GQFTGTAGA (SEQ 10.000 ID NO:99) 20 239 NQMNLGATL (SEQ 6.000 IDNO:151)

TABLE XIX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 2705 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 332 KRYFKLSHL (SEQ30000.000 ID NO:127) 2 362 RRFSRSDQL (SEQ ID 30000.000 NO:187) 3 416CRWPSCQKK (SEQ 10000.000 ID NO:50) 4 439 QRNMTKLQL (SEQ 2000.000 IDNO:173) 5 286 YRIHTHGVF (SEQ ID 1000.000 NO:252) 6 125 ARMFPNAPY (SEQ1000.000 ID NO:38) 7 294 FRGIQDVRR (SEQ ID 1000.000 NO:81) 8 432VRHHNMHQR (SEQ 1000.000 ID NO:243) 9 169 AQFPNHSFK (SEQ 1000.000 IDNO:36) 10 375 RRHTGVKPF (SEQ 900.000 ID NO:188) 11 126 RMFPNAPYL (SEQ750.000 ID NO:185) 12 144 IRNQGYSTV (SEQ ID 600.000 NO:117) 13 301RRVPGVAPT (SEQ 600.000 ID NO:189) 14 32 AQWAPVLDF (SEQ 500.000 ID NO:37)15 191 QQYSVPPPV (SEQ 300.000 ID NO:171) 16 373 HQRRHTGVK (SEQ 200.000ID NO:109) 17 426 ARSDELVRH (SEQ 200.000 ID NO:39) 18 383 FQCKTCQRK (SEQ200.000 ID NO:80) 19 239 NQMNLGATL (SEQ 200.000 ID NO:151) 20 389QRKFSRSDH (SEQ 200.000 ID NO:172)

TABLE XX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 3501 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 278 TPILCGAQY (SEQ ID40.000 NO:227) 2 141 QPAIRNQGY (SEQ 40.000 ID NO:170) 3 219 TPYSSDNLY(SEQ ID 40.000 NO:231) 4 327 YPGCNKRYF (SEQ 20.000 ID NO:250) 5 163TPSHHAAQF (SEQ 20.000 ID NO:228) 6 180 DPMGQQGSL (SEQ 20.000 ID NO:59) 7221 YSSDNLYQM (SEQ 20.000 ID NO:253) 8 26 LPVSGAAQW (SEQ 10.000 IDNO:138) 9 174 HSFKHEDPM (SEQ 10.000 ID NO:110) 10 82 EPHEEQCLS (SEQ ID6.000 NO:68) 11 213 QALLLRTPY (SEQ ID 6.000 NO:160) 12 119 QASSGQARM(SEQ 6.000 ID NO:161) 13 4 DVRDLNALL (SEQ 6.000 ID NO:62) 14 40FAPPGASAY (SEQ 6.000 ID NO:74) 15 120 ASSGQARMF (SEQ 5.000 ID NO:40) 16207 DSCTGSQAL (SEQ 5.000 ID NO:61) 17 303 VPGVAPTLV (SEQ 4.000 IDNO:242) 18 316 ETSEKRPFM (SEQ ID 4.000 NO:73) 19 152 VTFDGTPSY (SEQ ID4.000 NO:244) 20 412 KPFSCRWPS (SEQ ID 4.000 NO:123)

TABLE XXI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 3701 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 3 SDVRDLNAL (SEQ 40.000ID NO:206) 2 273 SDNHTTPIL (SEQ ID 40.000 NO:204) 3 81 AEPHEEQCL (SEQ ID10.000 NO:30) 4 298 QDVRRVPGV (SEQ 8.000 ID NO:164) 5 428 SDELVRHHN (SEQ6.000 ID NO:203) 6 85 EEQCLSAFT (SEQ ID 5.000 NO:65) 7 208 SCTGSQALL(SEQ ID 5.000 NO:202) 8 4 DVRDLNALL (SEQ 5.000 ID NO:62) 9 209 CTGSQALLL(SEQ ID 5.000 NO:52) 10 38 LDFAPPGAS (SEQ ID 4.000 NO:130) 11 223SDNLYQMTS (SEQ 4.000 ID NO:205) 12 179 EDPMGQQGS (SEQ 4.000 ID NO:64) 13206 TDSCTGSQA (SEQ 4.000 ID NO:220) 14 6 RDLNALLPA (SEQ 4.000 ID NO:177)15 84 HEEQCLSAF (SEQ ID 2.000 NO:107) 16 233 LECMTWNQM (SEQ 2.000 IDNO:131) 17 429 DELVRHHNM (SEQ 2.000 ID NO:53) 18 315 SETSEKRPF (SEQ ID2.000 NO:209) 19 349 GEKPYQCDF (SEQ 2.000 ID NO:91) 20 302 RVPGVAPTL(SEQ 1.500 ID NO:195)

TABLE XXII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 3801 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 437 MHQRNMTKL (SEQ36.000 ID NO:143) 2 434 HHNMHQRNM (SEQ 6.000 ID NO:108) 3 372 RHQRRHTGV(SEQ 6.000 ID NO:181) 4 180 DPMGQQGSL (SEQ 4.000 ID NO:59) 5 433RHHNMHQRN (SEQ 3.900 ID NO:180) 6 165 SHHAAQFPN (SEQ 3.900 ID NO:213) 7202 CHTPTDSCT (SEQ ID 3.000 NO:45) 8 396 DHLKTHTRT (SEQ 3.000 ID NO:57)9 161 GHTPSHHAA (SEQ 3.000 ID NO:94) 10 302 RVPGVAPTL (SEQ 2.600 IDNO:195) 11 417 RWPSCQKKF (SEQ 2.400 ID NO:196) 12 327 YPGCNKRYF (SEQ2.400 ID NO:250) 13 208 SCTGSQALL (SEQ ID 2.000 NO:202) 14 163 TPSHHAAQF(SEQ 2.000 ID NO:228) 15 120 ASSGQARMF (SEQ 2.000 ID NO:40) 16 18LGGGGGCAL (SEQ 2.000 ID NO:134) 17 177 KHEDPMGQQ (SEQ 1.800 ID NO:121)18 83 PHEEQCLSA (SEQ ID 1.800 NO:154) 19 10 ALLPAVPSL (SEQ ID 1.300NO:34) 20 225 NLYQMTSQL (SEQ 1.300 ID NO:147)

TABLE XXIII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 3901 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 437 MHQRNMTKL 135.000(SEQ ID NO:143) 2 332 KRYFKLSHL 45.000 (SEQ ID NO:127) 3 434 HHNMHQRNM30.000 (SEQ ID NO:108) 4 362 RRFSRSDQL 30.000 (SEQ ID NO:187) 5 372RHQRRHTGV 30.000 (SEQ ID NO:181) 6 10 ALLPAVPSL 9.000 (SEQ ID NO:34)  7439 QRNMTKLQL 7.500 (SEQ ID NO:173) 8 390 RKFSRSDHL 6.000 (SEQ IDNO:183) 9 396 DHLKTHTRT 6.000 (SEQ ID NO:57)  10 239 NQMNLGATL 6.000(SEQ ID NO:151) 11 423 KKFARSDEL 6.000 (SEQ ID NO:122) 12 126 RMFPNAPYL6.000 (SEQ ID NO:185) 13 225 NLYQMTSQL 6.000 (SEQ ID NO:147) 14 180DPMGQQGSL 6.000 (SEQ ID NO:59)  15 144 IRNQGYSTV 5.000 (SEQ ID NO:117)16 136 SCLESQPAI 4.000 (SEQ ID NO:198) 17 292 GVFRGIQDV 3.000 (SEQ IDNO:103) 18 302 RVPGVAPTL 3.000 (SEQ ID NO:195) 19 208 SCTGSQALL 3.000(SEQ ID NO:202) 20 207 DSCTGSQAL 3.000 (SEQ ID NO:61) 

TABLE XXIV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 3902 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 239 NQMNLGATL 24.000(SEQ ID NO:151) 2 390 RKFSRSDHL 20.000 (SEQ ID NO:183) 3 423 KKFARSDEL20.000 (SEQ ID NO:122) 4 32 AQWAPVLDF 5.000 (SEQ ID NO:37)  5 146NQGYSTVTF 5.000 (SEQ ID NO:150) 6 130 NAPYLPSCL 2.400 (SEQ ID NO:144) 7225 NLYQMTSQL 2.400 (SEQ ID NO:147) 8 30 GAAQWAPVL 2.400 (SEQ ID NO:86) 9 441 NMTKLQLAL 2.400 (SEQ ID NO:149) 10 302 RVPGVAPTL 2.400 (SEQ IDNO:195) 11 126 RMFPNAPYL 2.000 (SEQ ID NO:185) 12 218 RTPYSSDNL 2.000(SEQ ID NO:194) 13 209 CTGSQALLL 2.000 (SEQ ID NO:52)  14 332 KRYFKLSHL2.000 (SEQ ID NO:127) 15 180 DPMGQQGSL 2.000 (SEQ ID NO:59)  16 437MHQRNMTKL 2.000 (SEQ ID NO:143) 17 207 DSCTGSQAL 2.000 (SEQ ID NO:61) 18 208 SCTGSQALL 2.000 (SEQ ID NO:202) 19 329 GCNKRYFKL 2.000 (SEQ IDNO:90)  20 10 ALLPAVPSL 2.000 (SEQ ID NO:34) 

TABLE XXV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 4403 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 315 SETSEKRPF 80.000(SEQ ID NO:209) 2 349 GEKPYQCDF 80.000 (SEQ ID NO:91)  3 84 HEEQCLSAF60.000 (SEQ ID NO:107) 4 410 SEKPFSCRW 48.000 (SEQ ID NO:207) 5 429DELVRHHNM 24.000 (SEQ ID NO:53)  6 278 TPILCGAQY 15.000 (SEQ ID NO:227)7 141 QPAIRNQGY 9.000 (SEQ ID NO:170) 8 40 FAPPGASAY 9.000 (SEQ IDNO:74)  9 213 QALLLRTPY 9.000 (SEQ ID NO:160) 10 318 SEKRPFMCA 8.000(SEQ ID NO:208) 11 81 AEPHEEQCL 8.000 (SEQ ID NO:30)  12 152 VTFDGTPSY4.500 (SEQ ID NO:244) 13 101 TGTAGACRY 4.500 (SEQ ID NO:224) 14 120ASSGQARMF 4.500 (SEQ ID NO:40)  15 261 TEGQSNHST 4.000 (SEQ ID NO:221)16 85 EEQCLSAFT 4.000 (SEQ ID NO:65)  17 233 LECMTWNQM 4.000 (SEQ IDNO:131) 18 104 AGACRYGPF 4.000 (SEQ ID NO:31)  19 3 SDVRDLNAL 3.000 (SEQID NO:206) 20 185 QGSLGEQQY 3.000 (SEQ ID NO:166)

TABLE XXVI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 5101 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 303 VPGVAPTLV 314.600(SEQ ID NO:242) 2 180 DPMGQQGSL 242.000 (SEQ ID NO:59)  3 250 VAAGSSSSV157.300 (SEQ ID NO:236) 4 130 NAPYLPSCL 50.000 (SEQ ID NO:144) 5 30GAAQWAPVL 50.000 (SEQ ID NO:86)  6 20 GGGGCALPV 44.000 (SEQ ID NO:92)  764 PPPPPHSFI 40.000 (SEQ ID NO:157) 8 29 SGAAQWAPV 40.000 (SEQ IDNO:211) 9 18 LGGGGGCAL 31.460 (SEQ ID NO:134) 10 295 RGIQDVRRV 22.000(SEQ ID NO:179) 11 119 QASSGQARM 18.150 (SEQ ID NO:161) 12 418 WPSCQKKFA12.100 (SEQ ID NO:246) 13 82 EPHEEQCLS 12.100 (SEQ ID NO:68)  14 110GPFGPPPPS 11.000 (SEQ ID NO:96)  15 272 ESDNHTTPI 8.000 (SEQ ID NO:71) 16 306 VAPTLVRSA 7.150 (SEQ ID NO:237) 17 280 ILCGAQYRI 6.921 (SEQ IDNO:116) 18 219 TPYSSDNLY 6.600 (SEQ ID NO:231) 19 128 FPNAPYLPS 6.500(SEQ ID NO:79)  20 204 TPTDSCTGS 6.050 (SEQ ID NO:230)

TABLE XXVII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 5102 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 295 RGIQDVRRV 290.400(SEQ ID NO:179) 2 303 VPGVAPTLV 200.000 (SEQ ID NO:242) 3 180 DPMGQQGSL133.100 (SEQ ID NO:59)  4 250 VAAGSSSSV 110.000 (SEQ ID NO:236) 5 30GAAQWAPVL 55.000 (SEQ ID NO:86)  6 130 NAPYLPSCL 50.000 (SEQ ID NO:144)7 20 GGGGCALPV 44.000 (SEQ ID NO:92)  8 29 SGAAQWAPV 44.000 (SEQ IDNO:211) 9 64 PPPPPHSFI 40.000 (SEQ ID NO:157) 10 119 QASSGQARM 36.300(SEQ ID NO:161) 11 110 GPFGPPPPS 27.500 (SEQ ID NO:96)  12 412 KPFSCRWPS25.000 (SEQ ID NO:123) 13 18 LGGGGGCAL 24.200 (SEQ ID NO:134) 14 24CALPVSGAA 16.500 (SEQ ID NO:43)  15 219 TPYSSDNLY 15.000 (SEQ ID NO:231)16 292 GVFRGIQDV 14.641 (SEQ ID NO:103) 17 136 SCLESQPAI 14.520 (SEQ IDNO:198) 18 418 WPSCQKKFA 12.100 (SEQ ID NO:246) 19 269 TGYESDNHT 11.000(SEQ ID NO:225) 20 351 KPYQCDFKD 11.000 (SEQ ID NO:124)

TABLE XXVIII Results of BIMAS HLA Peptide Binding Prediction Analysisfor Binding of Human WT1 Peptides to Human HLA B 5201 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 191 QQYSVPPPV 100.000(SEQ ID NO:171) 2 32 AQWAPVLDF 30.000 (SEQ ID NO:37)  3 243 LGATLKGVA16.500 (SEQ ID NO:133) 4 303 VPGVAPTLV 13.500 (SEQ ID NO:242) 5 86EQCLSAFTV 12.000 (SEQ ID NO:69)  6 295 RGIQDVRRV 10.000 (SEQ ID NO:179)7 98 GQFTGTAGA 8.250 (SEQ ID NO:99)  8 292 GVFRGIQDV 8.250 (SEQ IDNO:103) 9 29 SGAAQWAPV 6.000 (SEQ ID NO:211) 10 146 NQGYSTVTF 5.500 (SEQID NO:150) 11 20 GGGGCALPV 5.000 (SEQ ID NO:92)  12 239 NQMNLGATL 4.000(SEQ ID NO:151) 13 64 PPPPPHSFI 3.600 (SEQ ID NO:157) 14 273 SDNHTTPIL3.300 (SEQ ID NO:204) 15 286 YRIHTHGVF 3.000 (SEQ ID NO:252) 16 269TGYESDNHT 3.000 (SEQ ID NO:225) 17 406 TGKTSEKPF 2.750 (SEQ ID NO:222)18 327 YPGCNKRYF 2.750 (SEQ ID NO:250) 19 7 DLNALLPAV 2.640 (SEQ IDNO:58)  20 104 AGACRYGPF 2.500 (SEQ ID NO:31) 

TABLE XXIX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA B 5801 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 230 TSQLECMTW 96.800(SEQ ID NO:234) 2 92 FTVHFSGQF 60.000 (SEQ ID NO:85)  3 120 ASSGQARMF40.000 (SEQ ID NO:40)  4 168 AAQFPNHSF 20.000 (SEQ ID NO:29)  5 408KTSEKPFSC 12.000 (SEQ ID NO:129) 6 394 RSDHLKTHT 9.900 (SEQ ID NO:192) 7276 HTTPILCGA 7.200 (SEQ ID NO:115) 8 218 RTPYSSDNL 6.600 (SEQ IDNO:194) 9 152 VTFDGTPSY 6.000 (SEQ ID NO:244) 10 40 FAPPGASAY 6.000 (SEQID NO:74)  11 213 QALLLRTPY 4.500 (SEQ ID NO:160) 12 347 HTGEKPYQC 4.400(SEQ ID NO:112) 13 252 AGSSSSVKW 4.400 (SEQ ID NO:32)  14 211 GSQALLLRT4.356 (SEQ ID NO:102) 15 174 HSFKHEDPM 4.000 (SEQ ID NO:110) 16 317TSEKRPFMC 4.000 (SEQ ID NO:233) 17 26 LPVSGAAQW 4.000 (SEQ ID NO:138) 18289 HTHGVFRGI 3.600 (SEQ ID NO:113) 19 222 SSDNLYQMT 3.300 (SEQ IDNO:217) 20 96 FSGQFTGTA 3.300 (SEQ ID NO:82) 

TABLE XXX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA CW0301 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 10 ALLPAVPSL 100.000(SEQ ID NO:34)  2 332 KRYFKLSHL 48.000 (SEQ ID NO:127) 3 126 RMFPNAPYL36.000 (SEQ ID NO:185) 4 3 SDVRDLNAL 30.000 (SEQ ID NO:206) 5 239NQMNLGATL 24.000 (SEQ ID NO:151) 6 225 NLYQMTSQL 24.000 (SEQ ID NO:147)7 180 DPMGQQGSL 20.000 (SEQ ID NO:59)  8 362 RRFSRSDQL 12.000 (SEQ IDNO:187) 9 329 GCNKRYFKL 10.000 (SEQ ID NO:90)  10 286 YRIHTHGVF 10.000(SEQ ID NO:252) 11 301 RRVPGVAPT 10.000 (SEQ ID NO:189) 12 24 CALPVSGAA10.000 (SEQ ID NO:43)  13 136 SCLESQPAI 7.500 (SEQ ID NO:198) 14 437MHQRNMTKL 7.200 (SEQ ID NO:143) 15 390 RKFSRSDHL 6.000 (SEQ ID NO:183)16 423 KKFARSDEL 6.000 (SEQ ID NO:122) 17 92 FTVHFSGQF 5.000 (SEQ IDNO:85)  18 429 DELVRHHNM 5.000 (SEQ ID NO:53)  19 130 NAPYLPSCL 4.800(SEQ ID NO:144) 20 30 GAAQWAPVL 4.000 (SEQ ID NO:86) 

TABLE XXXI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA CW0401 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 356 DFKDCERRF 120.000(SEQ ID NO:55)  2 334 YFKLSHLQM 100.000 (SEQ ID NO:248) 3 180 DPMGQQGSL88.000 (SEQ ID NO:59)  4 163 TPSHHAAQF 52.800 (SEQ ID NO:228) 5 327YPGCNKRYF 40.000 (SEQ ID NO:250) 6 285 QYRIHTHGV 27.500 (SEQ ID NO:175)7 424 KFARSDELV 25.000 (SEQ ID NO:119) 8 326 AYPGCNKRY 25.000 (SEQ IDNO:42)  9 192 QYSVPPPVY 25.000 (SEQ ID NO:176) 10 417 RWPSCQKKF 22.000(SEQ ID NO:196) 11 278 TPILCGAQY 12.000 (SEQ ID NO:227) 12 10 ALLPAVPSL11.616 (SEQ ID NO:34)  13 141 QPAIRNQGY 11.000 (SEQ ID NO:170) 14 303VPGVAPTLV 11.000 (SEQ ID NO:242) 15 219 TPYSSDNLY 10.000 (SEQ ID NO:231)16 39 DFAPPGASA 7.920 (SEQ ID NO:54)  17 99 QFTGTAGAC 6.000 (SEQ IDNO:165) 18 4 DVRDLNALL 5.760 (SEQ ID NO:62)  19 70 SFIKQEPSW 5.500 (SEQID NO:210) 20 63 PPPPPPHSF 5.280 (SEQ ID NO:158)

TABLE XXXII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Human HLA CW0602 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 332 KRYFKLSHL 9.680 (SEQID NO:127) 2 239 NQMNLGATL 6.600 (SEQ ID NO:151) 3 130 NAPYLPSCL 6.600(SEQ ID NO:144) 4 7 DLNALLPAV 6.000 (SEQ ID NO:58)  5 441 NMTKLQLAL6.000 (SEQ ID NO:149) 6 225 NLYQMTSQL 6.000 (SEQ ID NO:147) 7 4DVRDLNALL 6.000 (SEQ ID NO:62)  8 3 SDVRDLNAL 4.400 (SEQ ID NO:206) 9 10ALLPAVPSL 4.000 (SEQ ID NO:34)  10 213 QALLLRTPY 3.300 (SEQ ID NO:160)11 319 EKRPFMCAY 3.000 (SEQ ID NO:67)  12 30 GAAQWAPVL 2.200 (SEQ IDNO:86)  13 242 NLGATLKGV 2.200 (SEQ ID NO:146) 14 292 GVFRGIQDV 2.200(SEQ ID NO:103) 15 207 DSCTGSQAL 2.200 (SEQ ID NO:61)  16 362 RRFSRSDQL2.200 (SEQ ID NO:187) 17 439 QRNMTKLQL 2.200 (SEQ ID NO:173) 18 295RGIQDVRRV 2.200 (SEQ ID NO:179) 19 423 KKFARSDEL 2.200 (SEQ ID NO:122)20 180 DPMGQQGSL 2.200 (SEQ ID NO:59) 

TABLE XXXIII Results of BIMAS HLA Peptide Binding Prediction Analysisfor Binding of Human WT1 Peptides to Human HLA CW0702 Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 319 EKRPFMCAY 26.880(SEQ ID NO:67)  2 326 AYPGCNKRY 24.000 (SEQ ID NO:42)  3 40 FAPPGASAY14.784 (SEQ ID NO:74)  4 192 QYSVPPPVY 12.000 (SEQ ID NO:176) 5 278TPILCGAQY 12.000 (SEQ ID NO:227) 6 219 TPYSSDNLY 12.000 (SEQ ID NO:231)7 213 QALLLRTPY 8.800 (SEQ ID NO:160) 8 125 ARMFPNAPY 8.000 (SEQ IDNO:38)  9 327 YPGCNKRYF 6.600 (SEQ ID NO:250) 10 152 VTFDGTPSY 5.600(SEQ ID NO:244) 11 141 QPAIRNQGY 4.800 (SEQ ID NO:170) 12 345 RKHTGEKPY4.000 (SEQ ID NO:184) 13 185 QGSLGEQQY 4.000 (SEQ ID NO:166) 14 101TGTAGACRY 4.000 (SEQ ID NO:224) 15 375 RRHTGVKPF 4.000 (SEQ ID NO:188)16 263 GQSNHSTGY 4.000 (SEQ ID NO:100) 17 163 TPSHHAAQF 3.000 (SEQ IDNO:228) 18 33 QWAPVLDFA 2.688 (SEQ ID NO:174) 19 130 NAPYLPSCL 2.640(SEQ ID NO:144) 20 84 HEEQCLSAF 2.400 (SEQ ID NO:107)

TABLE XXXIV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Mouse MHC Class I Db Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 235 CMTWNQMNL 5255.712(SEQ ID NO:49)  2 126 RMFPNAPYL 1990.800 (SEQ ID NO:185) 3 221 YSSDNLYQM930.000 (SEQ ID NO:253) 4 228 QMTSQLECM 33.701 (SEQ ID NO:169) 5 239NQMNLGATL 21.470 (SEQ ID NO:151) 6 441 NMTKLQLAL 19.908 (SEQ ID NO:149)7 437 MHQRNMTKL 19.837 (SEQ ID NO:143) 8 136 SCLESQPAI 11.177 (SEQ IDNO:198) 9 174 HSFKHEDPM 10.800 (SEQ ID NO:110) 10 302 RVPGVAPTL 10.088(SEQ ID NO:195) 11 130 NAPYLPSCL 8.400 (SEQ ID NO:144) 12 10 ALLPAVPSL5.988 (SEQ ID NO:34)  13 208 SCTGSQALL 4.435 (SEQ ID NO:202) 14 209CTGSQALLL 3.548 (SEQ ID NO:52)  15 238 WNQMNLGAT 3.300 (SEQ ID NO:245)16 218 RTPYSSDNL 3.185 (SEQ ID NO:194) 17 24 CALPVSGAA 2.851 (SEQ IDNO:43)  18 18 LGGGGGCAL 2.177 (SEQ ID NO:134) 19 142 PAIRNQGYS 2.160(SEQ ID NO:152) 20 30 GAAQWAPVL 1.680 (SEQ ID NO:86) 

TABLE XXXV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Mouse MHC Class I Dd Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 112 FGPPPPSQA 48.000(SEQ ID NO:76)  2 122 SGQARMFPN 36.000 (SEQ ID NO:212) 3 104 AGACRYGPF30.000 (SEQ ID NO:31)  4 218 RTPYSSDNL 28.800 (SEQ ID NO:194) 5 130NAPYLPSCL 20.000 (SEQ ID NO:144) 6 302 RVPGVAPTL 20.000 (SEQ ID NO:195)7 18 LGGGGGCAL 20.000 (SEQ ID NO:134) 8 81 AEPHEEQCL 10.000 (SEQ IDNO:30)  9 29 SGAAQWAPV 7.200 (SEQ ID NO:211) 10 423 KKFARSDEL 7.200 (SEQID NO:122) 11 295 RGIQDVRRV 7.200 (SEQ ID NO:179) 12 390 RKFSRSDHL 6.000(SEQ ID NO:183) 13 332 KRYFKLSHL 6.000 (SEQ ID NO:127) 14 362 RRFSRSDQL6.000 (SEQ ID NO:187) 15 417 RWPSCQKKF 6.000 (SEQ ID NO:196) 16 160YGHTPSHHA 6.000 (SEQ ID NO:249) 17 20 GGGGCALPV 6.000 (SEQ ID NO:92)  18329 GCNKRYFKL 5.000 (SEQ ID NO:90)  19 372 RHQRRHTGV 4.500 (SEQ IDNO:181) 20 52 GGPAPPPAP 4.000 (SEQ ID NO:93) 

TABLE XXXVI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Mouse MHC Class I Kb Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 329 GCNKRYFKL 24.000(SEQ ID NO:90) 2 225 NLYQMTSQL 10.000 (SEQ ID NO:147) 3 420 SCQKKFARS3.960 (SEQ ID NO:200) 4 218 RTPYSSDNL 3.630 (SEQ ID NO:194) 5 437MHQRNMTKL 3.600 (SEQ ID NO:143) 6 387 TCQRKFSRS 3.600 (SEQ ID NO:219) 7302 RVPGVAPTL 3.300 (SEQ ID NO:195) 8 130 NAPYLPSCL 3.000 (SEQ ID NO:144) 9 289 HTHGVFRGI 3.000 (SEQ ID NO:113) 10 43 PGASAYGSL 2.400 (SEQ IDNO:153) 11 155 DGTPSYGHT 2.400 (SEQ ID NO:56) 12 273 SDNHTTPIL 2.200(SEQ ID NO:204) 13 126 RMFPNAPYL 2.200 (SEQ ID NO:185) 14 128 FPNAPYLPS2.000 (SEQ ID NO:79) 15 3 SDVRDLNAL 1.584 (SEQ ID NO:206) 16 207DSCTGSQAL 1.584 (SEQ ID NO:61) 17 332 KRYFKLSHL 1.500 (SEQ ID NO:127) 1818 LGGGGGCAL 1.320 (SEQ ID NO:134) 19 233 LECMTWNQM 1.320 (SEQ IDNO:131) 20 441 NMTKLQLAL 1.200 (SEQ ID NO:149)

TABLE XXXVII Results of BIMAS HLA Peptide Binding Prediction Analysisfor Binding of Human WT1 Peptides to Mouse MHC Class I Kd Score(Estimate of Half Time of Start Subsequence Residue Disassociation of aMolecule Rank Position Listing Containing This Subsequence) 1 285QYRIHTHGV 600.000 (SEQ ID NO:175) 2 424 KFARSDELV 288.000 (SEQ IDNO:119) 3 334 YFKLSHLQM 120.000 (SEQ ID NO:248) 4 136 SCLESQPTI 115.200(SEQ ID NO: 199) 5 239 NQMNLGATL 115.200 (SEQ ID NO:151) 6 10 ALLPAVSSL115.200 (SEQ NO:35) 7 47 AYGSLGGPA 86.400 (SEQ ID NO:41) 8 180 DPMGQQGSL80.000 (SEQ ID NO:59) 9 270 GYESDNHTA 72.000 (SEQ ID NO:105) 10 326AYPGCNKRY 60.000 (SEQ ID NO:42) 11 192 QYSVPPPVY 60.000 (SEQ ID NO:176)12 272 ESDNHTAPI 57.600 (SEQ ID NO:70) 13 289 HTHGVFRGI 57.600 (SEQ IDNO:113) 14 126 DVRDLNALL 57.600 (SEQ ID NO:62) 15 4 CTGSQALLL 57.600(SEQ ID NO: 52) 16 208 SCTGSQALL 48.000 (SEQ ID NO:202) 17 441 NMTKLQLAL48.000 (SEQ ID NO:149) 18 207 DSCTGSQAL 48.000 (SEQ ID NO:61) 19 130NAPYLPSCL 48.000 (SEQ ID NO:144) 20 235 CMTWNQMNL 48.000 (SEQ ID NO:49)

TABLE XXXVIII Results of BIMAS HLA Peptide Binding Prediction Analysisfor Binding of Human WT1 Peptides to Mouse MHC Class I Kk Score(Estimate of Half Time of Start Subsequence Residue Disassociation of aMolecule Rank Position Listing Containing This Subsequence) 1 81AEPHEEQCL 40.000 (SEQ ID NO:30) 2 85 EEQCLSAFT 40.000 (SEQ ID NO:65) 3429 DELVRHHNM 20.000 (SEQ ID NO:53) 4 315 SETSEKRPF 20.000 (SEQ IDNO:209) 5 261 TEGQSNHST 20.000 (SEQ ID NO:221) 6 410 SEKPFSCRW 10.000(SEQ ID NO:207) 7 272 ESDNHTTPI 10.000 (SEQ ID NO:71) 8 318 SEKRPFMCA10.000 (SEQ ID NO:208) 9 138 LESQPAIRN 10.000 (SEQ ID NO:132) 10 233LECMTWNQM 10.000 (SEQ ID NO:131) 11 298 QDVRRVPGV 10.000 (SEQ ID NO:164)12 84 HEEQCLSAF 10.000 (SEQ ID NO:107) 13 349 GEKPYQCDF 10.000 (SEQ IDNO:91) 14 289 HTHGVFRGI 10.000 (SEQ ID NO:113) 15 179 EDPMGQQGS 8.000(SEQ ID NO:64) 16 136 SCLESQPAI 5.000 (SEQ ID NO:198) 17 280 LLCGAQYRI5.000 (SEQ ID NO:116) 18 273 SDNHTTPIL 4.000 (SEQ ID NO:204) 19 428SDELVRHHN 4.000 (SEQ ID NO:203) 20 3 SDVRDLNAL 4.000 (SEQ ID NO:206)

TABLE XXXIX Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Mouse MHC Class I Ld Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 163 TPSHHAAQF 360.000(SEQ ID NO:228) 2 327 YPGCNKRYF 300.000 (SEQ ID NO:250) 3 180 DPMGQQGSL150.000 (SEQ ID NO:59) 4 26 LPVSGAAQW 93.600 (SEQ ID NO:138) 5 278TPILCGAQY 72.000 (SEQ ID NO:227) 6 141 QPAIRNQGY 60.000 (SEQ ID NO:170)7 219 TPYSSDNLY 60.000 (SEQ ID NO:231) 8 303 VPGVAPTLV 60.000 (SEQ IDNO:242) 9 120 ASSGQARMF 50.000 (SEQ ID NO:40) 10 63 PPPPPPHSF 45.000(SEQ ID NO:158) 11 113 GPPPPSQAS 45.000 (SEQ ID NO:97) 12 157 TPSYGHTPS39.000 (SEQ ID NO:229) 13 207 DSCTGSQAL 32.500 (SEQ ID NO:61) 14 110GPFGPPPPS 30.000 (SEQ ID NO:96) 15 82 EPHEEQCLS 30.000 (SEQ ID NO:68) 16412 KPFSCRWPS 30.000 (SEQ ID NO:123) 17 418 WPSCQKKFA 30.000 (SEQ IDNO:246) 18 221 YSSDNLYQM 30.000 (SEQ ID NO:253) 19 204 TPTDSCTGS 30.000(SEQ ID NO:230) 20 128 FPNAPYLPS 30.000 (SEQ ID NO:79)

TABLE XL Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Human WT1 Peptides to Cattle HLA A20 Score (Estimate of HalfTime of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 350 EKPYQCDFK 1000.00(SEQ ID NO:66) 2 319 EKRPFMCAY 500.000 (SEQ ID NO:67) 3 423 KKFARSDEL500.000 (SEQ ID NO:122) 4 345 RKHTGEKPY 500.000 (SEQ ID NO:184) 5 390RKFSRSDHL 500.000 (SEQ ID NO:183) 6 137 CLESQPAIR 120.000 (SEQ ID NO:47)7 380 VKPFQCKTC 100.000 (SEQ ID NO:239) 8 407 GKTSEKPFS 100.000 (SEQ IDNO:95) 9 335 FKLSHLQMH 100.000 (SEQ ID NO:78) 10 247 LKGVAAGSS 100.000(SEQ ID NO:135) 11 370 LKRHQRRHT 100.000 (SEQ ID NO:136) 12 258VKWTEGQSN 100.000 (SEQ ID NO:240) 13 398 LKTHTRTHT 100.000 (SEQ IDNO:137) 14 331 NKRYFKLSH 100.000 (SEQ ID NO:145) 15 357 FKDCERRFS100.000 (SEQ ID NO:77) 16 385 CKTCQRKFS 100.000 (SEQ ID NO:46) 17 294FRGIQDVRR 80.000 (SEQ ID NO:81) 18 368 DQLKRHQRR 80.000 (SEQ ID NO:60)19 432 VRHHNMHQR 80.000 (SEQ ID NO:243) 20 118 SQASSGQAR 80.000 (SEQ IDNO:216)

TABLE XLI Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Mouse WT1 Peptides to Mouse MHC Class I A 0201 Score(Estimate of Half Time of Start Subsequence Residue Disassociation of aMolecule Rank Position Listing Containing This Subsequence) 1 126RMFPNAPYL 313.968 (SEQ ID NO:293) 2 187 SLGEQQYSV 285.163 (SEQ IDNO:299) 3 10 ALLPAVSSL 181.794 (SEQ NO:255) 4 225 NLYQMTSQL 68.360 (SEQID NO:284) 5 292 GVFRGIQDV 51.790 (SEQ ID NO:270) 6 93 TLHFSGQFT 40.986(SEQ ID NO:302) 7 191 QQYSVPPPV 22.566 (SEQ ID NO:290) 8 280 ILCGAQYRI17.736 (SEQ ID NO:274) 9 441 NMTKLHVAL 15.428 (SEQ ID NO:285) 10 235CMTWNQMNL 15.428 (SEQ ID NO:258) 11 7 DLNALLPAV 11.998 (SEQ ID NO:261)12 242 NLGATLKGM 11.426 (SEQ ID NO:283) 13 227 YQMTSQLEC 8.573 (SEQ IDNO:307) 14 239 NQMNLGATL 8.014 (SEQ ID NO:286) 15 309 TLVRSASET 7.452(SEQ ID NO:303) 16 408 KTSEKPFSC 5.743 (SEQ ID NO:277) 17 340 LQMHSRKHT4.752 (SEQ ID ID NO:280) 18 228 QMTSQLECM 4.044 (SEQ ID NO:289) 19 37VLDFAPPGA 3.378 (SEQ ID NO:304) 20 302 RVSGVAPTL 1.869 (SEQ ID NO:295)

TABLE XLII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Mouse WT1 Peptides to Mouse MHC Class I Db Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 221 YSSDNLYQM 312.000(SEQ ID NO:308) 2 126 RMFPNAPYL 260.000 (SEQ ID NO:293) 3 235 CMTWNQMNL260.000 (SEQ ID NO:258) 4 437 MHQRNMTKL 200.000 (SEQ ID NO:281) 5 238WNQMNLGAT 12.000 (SEQ ID NO:305) 6 130 NAPYLPSCL 8.580 (SEQ ID NO:282) 73 SDVRDLNAL 7.920 (SEQ ID NO:298) 8 136 SCLESQPTI 7.920 (SEQ ID NO:296)9 81 AEPHEEQCL 6.600 (SEQ ID NO:254) 10 10 ALLPAVSSL 6.600 (SEQ IDNO:255) 11 218 RTPYSSDNL 6.000 (SEQ ID NO:294) 12 441 NMTKLHVAL 3.432(SEQ ID NO:285) 13 228 QMTSQLECM 3.120 (SEQ ID NO:289) 14 174 HSFKHEDPM3.120 (SEQ ID NO:272) 15 242 NLGATLKGM 2.640 (SEQ ID NO:283) 16 261TEGQSNHGI 2.640 (SEQ ID NO:301) 17 225 NLYQMTSQL 2.640 (SEQ ID NO:284)18 207 DSCTGSQAL 2.600 (SEQ ID NO:263) 19 119 QASSGQARM 2.600 (SEQ IDNO:288) 20 18 LGGGGGCGL 2.600 (SEQ ID NO:279)

TABLE XLIII Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Mouse WT1 Peptides to Mouse MHC Class I Kb Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 329 GCNKRYFKL 24.000(SEQ ID NO:268) 2 225 NLYQMTSQL 10.000 (SEQ ID NO:284) 3 420 SCQKKFARS3.960 (SEQ ID NO:297) 4 218 RTPYSSDNL 3.630 (SEQ ID NO:294) 5 437MLTQRNMTKL 3.600 (SEQ ID NO:281) 6 387 TCQRKFSRS 3.600 (SEQ ID NO:300) 7289 HTHGVFRGI 3.000 (SEQ ID NO:273) 8 130 NAPYLPSCL 3.000 (SEQ IDNO:282) 9 43 PGASAYGSL 2.400 (SEQ ID NO:287) 10 155 DGAPSYGHT 2.400 (SEQID NO:260) 11 126 RMFPNAPYL 2.200 (SEQ ID NO:293) 12 128 FPNAPYLPS 2.000(SEQ ID NO:267) 13 207 DSCTGSQAL 1.584 (SEQ ID NO:263) 14 3 SDVRDLNAL1.584 (SEQ ID NO:298) 15 332 KRYFKLSHL 1.500 (SEQ ID NO:276) 16 233LECMTWNQM 1.320 (SEQ ID NO:278) 17 18 LGGGGGCGL 1.320 (SEQ ID NO:279) 18242 NLGATLKGM 1.200 (SEQ ID NO:283) 19 123 GQARMFPN 1.200 (SEQ IDNO:269)A 20 441 NMTKLHVAL 1.200 (SEQ ID NO:285)

TABLE XLIV Results of BIMAS HLA Peptide Binding Prediction Analysis forBinding of Mouse WT1 Peptides to Mouse MHC Class I Kd Score (Estimate ofHalf Time of Start Subsequence Residue Disassociation of a Molecule RankPosition Listing Containing This Subsequence) 1 285 QYRIHTHGV 600.000(SEQ ID NO:291) 2 424 KFARSDELV 288.000 (SEQ ID NO:275) 3 334 YFKLSHLQM120.000 (SEQ ID NO:306) 4 136 SCLESQPTI 115.200 (SEQ ID NO:296) 5 239NQMNLGATL 115.200 (SEQ ID NO:286) 6 10 ALLPAVSSL 115.200 (SEQ ID NO:255)7 47 AYGSLGGPA 86.400 (SEQ ID NO:256) 8 180 DPMGQQGSL 80.000 (SEQ IDNO:262) 9 270 GYESDNHTA 72.000 (SEQ ID NO:271) 10 192 QYSVPPPVY 60.000(SEQ ID NO:292) 11 326 AYPGCNKRY 60.000 (SEQ ID NO:257) 12 289 HTHGVFRGI57.600 (SEQ ID NO:273) 13 4 DVRDLNALL 57.600 (SEQ ID NO:264) 14 126RMFPNAPYL 57.600 (SEQ ID NO:293) 15 209 CTGSQALLL 48.000 (SEQ ID NO:259)16 86 EQCLSAFTL 48.000 (SEQ ID NO:265) 17 302 RVSGVAPTL 48.000 (SEQ IDNO:295) 18 218 RTPYSSDNL 48.000 (SEQ ID NO:294) 19 272 ESDNHTAPI 48.000(SEQ ID NO:266) 20 225 NLYQMTSQL 48.000 (SEQ ID NO:284)

TABLE XLV Results of TSites Peptide Binding Prediction Analysis forHuman WT1 Peptides Capable of Eliciting a Helper T cell Response PeptideSequence p6–23 RDLNALLPAVPSLGGGG (SEQ ID NO:1) p30–35 GAAQWA (SEQ IDNO:309) p45–56 ASAYGSLGGPAP (SEQ ID NO:310) p91–105 AFTVHFSGQFTGTAG (SEQID NO:311) p117–139 PSQASSGQARMFPNAPYLPSCLE (SEQ ID NO:2) p167–171 HAAQF(SEQ ID NO:312) p202–233 CHTPTDSCTGSQALLLRTPYSSDNLYQMTSQL (SEQ IDNO:313) p244–262 GATLKGVAAGSSSSVKWTE (SEQ ID NO:4) p287–318RIHTHGVFRGIQDVRRVPGVAPTLVRSASETS (SEQ ID NO:314) p333–336 RYFK (SEQ IDNO:315) p361–374 ERRFSRSDQLKRHQ (SEQ ID NO:316) p389–410QRKFSRSDHLKTHTRTHTGKTS (SEQ ID NO:317) p421–441 CQKKFARSDELVRHHNMHQRN(SEQ ID NO:318)

Certain CTL peptides (shown in Table XLVI) were selected for furtherstudy. For each peptide in Table XLVI, scores obtained using BIMAS HLApeptide binding prediction analysis are provided.

TABLE XLVI WT1 Peptide Sequences and HLA Peptide Binding PredictionsPeptide Sequence Comments p329–337 GCNKRYFKL Score 24,000 (SEQ ID NOs:90 and 268) p225–233 NLYQMTSQL binds also to class II and (SEQ ID NOs:147 and HLA A2, Kd, score 10,000 284) p235–243 CMTWNQMNL binds also toHLA A2, (SEQ ID NOs: 49 and score 5,255,712 258) p126–134 RMFPNAPYLbinds also to Kd, class II (SEQ ID NOs: 185 and and HLA A2, score 293)1,990,800 p221–229 YSSDNLYQM binds also to Ld, score (SEQ ID NOs: 253and 312,000 308) p228–236 QMTSQLECM score 3,120 (SEQ ID NOs: 169 and289) p239–247 NQMNLGATL binds also to HLA A 0201, (SEQ ID NOs: 151 andKd, score 8,015 286) mouse p136–144 SCLESQPTI binds also to Kd, 1 (SEQID NO:296) mismatch to human human p136–144 SCLESQPAI score 7,920 (SEQID NO:198) mouse p10–18 ALLPAVSSL binds also to Kd, HLA A2, (SEQ IDNO:255) 1 mismatch to human human p10–18 ALLPAVPSL score 6,600 (SEQ IDNO:34)

Peptide binding to C57B1/6 murine MHC was confirmed using the leukemiacell line RMA-S, as described by Ljunggren et al., Nature 346:476–480,1990. In brief, RMA-S cells were cultured for 7 hours at 26° C. incomplete medium supplemented with 1% FCS. A total of 10⁶ RMA-S cellswere added into each well of a 24-well plate and incubated either aloneor with the designated peptide (25 ug/ml) for 16 hours at 26° C. andadditional 3 hours at 37° C. in complete medium. Cells were then washedthree times and stained with fluorescein isothiocyanate-conjugated antiD^(b) or anti-K^(b) antibody (PharMingen, San Diego, Calif.). Labeledcells were washed twice, resuspended and fixed in 500 ul of PBS with 1%paraformaldehyde and analyzed for fluorescence intensity in a flowcytometer (Becton-Dickinson FACSCalibur®). The percentage of increase ofD^(b) or K^(b) molecules on the surface of the RMA-S cells was measuredby increased mean fluorescent intensity of cells incubated with peptidecompared with that of cells incubated in medium alone.

Mice were immunized with the peptides capable of binding to murine classI MHC. Following immunization, spleen cells were stimulated in vitro andtested for the ability to lyse targets incubated with WT1 peptides. CTLwere evaluated with a standard chromium release assay (Chen et al.,Cancer Res. 54:1065–1070, 1994). 10⁶ target cells were incubated at 37°C. with 150 μCi of sodium ⁵¹Cr for 90 minutes, in the presence orabsence of specific peptides. Cells were washed three times andresuspended in RPMI with 5% fetal bovine serum. For the assay, 10⁴⁵¹Cr-labeled target cells were incubated with different concentrationsof effector cells in a final volume of 200 μl in U-bottomed 96-wellplates. Supernatants were removed after 4 to 7 hours at 37° C., and thepercentage specific lysis was determined by the formula:% specific lysis=100×(experimental release−spontaneous release)/(maximumrelease−spontaneous release).

The results, presented in Table XLVII, show that some WT1 peptides canbind to class I MHC molecules, which is essential for generating CTL.Moreover, several of the peptides were able to elicit peptide specificCTL (FIGS. 9A and 9B), as determined using chromium release assays.Following immunization to CTL peptides p10–18 human, p136–144 human,p136–144 mouse and p235–243, peptide specific CTL lines were generatedand clones were established. These results indicate that peptidespecific CTL can kill malignant cells expressing WT1.

TABLE XLVII Binding of WT1 CTL Peptides to mouse B6 class I antigensPeptide Binding Affinity to Mouse MHC Class I Positive control 91%negative control  0.5.–1.3% p235–243 33.6% p136–144 mouse 27.9% p136–144human 52% p10–18: human  2.2% p225–233  5.8% p329–337  1.2% p126–134 0.9% p221–229  0.8% p228–236  1.2% p239–247  1%

Example 5 Use of a WT1 Polypeptide to Elicit WT1 Specific CTL in Mice

This Example illustrates the ability of a representative WT1 polypeptideto elicit CTL immunity capable of killing WT1 positive tumor cell lines.

P117–139, a peptide with motifs appropriate for binding to class I andclass II MHC, was identified as described above using TSITES and BIMASHLA peptide binding prediction analyses. Mice were immunized asdescribed in Example 3. Following immunization, spleen cells werestimulated in vitro and tested for the ability to lyse targets incubatedwith WT1 peptides, as well as WT1 positive and negative tumor cells. CTLwere evaluated with a standard chromium release assay. The results,presented in FIGS. 10A–10D, show that P117 can elicit WT1 specific CTLcapable of killing WT1 positive tumor cells, whereas no killing of WT1negative cells was observed. These results demonstrate that peptidespecific CTL in fact kill malignant cells expressing WT1 and thatvaccine and T cell therapy are effective against malignancies thatexpress WT1.

Similar immunizations were performed using the 9-mer class I MHC bindingpeptides p136–144, p225–233, p235–243 as well as the 23-mer peptidep117–139. Following immunization, spleen cells were stimulated in vitrowith each of the 4 peptides and tested for ability to lyse targetsincubated with WT1 peptides. CTL were generated specific for p136–144,p235–243 and p117–139, but not for p225–233. CTL data for p235–243 andp117–139 are presented in FIGS. 11A and 11B. Data for peptides p136–144and p225–233 are not depicted.

CTL lysis demands that the target WT1 peptides are endogenouslyprocessed and presented in association with tumor cell class I MHCmolecules. The above WT1 peptide specific CTL were tested for ability tolyse WT1 positive versus negative tumor cell lines. CTL specific forp235–243 lysed targets incubated with the p235–243 peptides, but failedto lyse cell lines that expressed WT1 proteins (FIG. 11A). By markedcontrast, CTL specific for p117–139 lysed targets incubated withp117–139 peptides and also lysed malignant cells expressing WT1 (FIG.11B). As a negative control, CTL specific for p117–139 did not lyse WT1negative EL-4 (also referred to herein as E10).

Specificity of WT1 specific lysis was confirmed by cold targetinhibition (FIGS. 12A–12B). Effector cells were plated for variouseffector: target ratios in 96-well U-bottom plates. A ten-fold excess(compared to hot target) of the indicated peptide-coated target without⁵¹Cr labeling was added. Finally, 10⁴ ⁵¹Cr-labeled target cells per wellwere added and the plates incubated at 37° C. for 4 hours. The totalvolume per well was 200 μl.

Lysis of TRAMP-C by p117–139 specific CTL was blocked from 58% to 36% byEL-4 incubated with the relevant peptide p117–139, but not with EL-4incubated with an irrelevant peptide (FIG. 12A). Similarly, lysis ofBLK-SV40 was blocked from 18% to 0% by EL-4 incubated with the relevantpeptide p117–139 (FIG. 12B). Results validate that WT1 peptide specificCTL specifically kill malignant cells by recognition of processed WT1.

Several segments with putative CTL motifs are contained within p117–139.To determine the precise sequence of the CTL epitope all potential 9-merpeptides within p117–139 were synthesized (Table XLVIII). Two of thesepeptides (p126–134 and p130–138) were shown to bind to H-2^(b) class Imolecules (Table XLVIII). CTL generated by immunization with p117–139lysed targets incubated with p126–134 and p130–138, but not the other9-mer peptides within p117–139 (FIG. 13A).

The p117–139 specific CTL line was restimulated with either p126–134 orp130–138. Following restimulation with p126–134 or p130–138, both T celllines demonstrated peptide specific lysis, but only p130–138 specificCTL showed lysis of a WT1 positive tumor cell line (FIGS. 13B and 13C).Thus, p130–138 appears to be the naturally processed epitope.

TABLE XLVIII Binding of WT1 CTL 9mer Peptides within p117–139 to mouseB6 class I antigens Binding Affinity to Peptide Mouse MHC Class IP117–125 PSQASSGQA (SEQ ID 2% NO:221) P118–126 SQASSGQAR (SEQ ID 2%NO:216) P119–127 QASSGQARM (SEQ ID 2% NOs: 161 and 288) P120–128ASSGQARMF (SEQ ID 1% NO:40 P121–129 SSGQARMFP (SEQ ID 1% NO 222)P122–130 SGQARMFPN (SEQ ID 1% NO:212) P123–131 GQARMFPNA (SEQ ID 1% NOs:98 and 269) P124–132 QARMFPNAP (SEQ ID 1% NO:223) P125–133 ARMFPNAPY(SEQ ID 1% NO:38) P126–134 RMFPNAPYL (SEQ ID 79%  NOs: 185 and 293)P127–135 MFPNAPYLP (SEQ ID 2% NO:224) P128–136 FPNAPYLPS (SEQ ID 1%NOs:79 and 267) P129–137 PNAPYLPSC (SEQ ID 1% NO:225) P130–138 NAPYLPSCL(SEQ ID 79%  NOs: 144 and 282) P131–139 APYLPSCLE (SEQ ID 1% NO:226)

Example 6 Identification of WT1 Specific mRNA in Mouse Tumor Cell Lines

This Example illustrates the use of RT-PCR to detect WT1 specific mRNAin cells and cell lines.

Mononuclear cells were isolated by density gradient centrifugation, andwere immediately frozen and stored at −80° C. until analyzed by RT-PCRfor the presence of WT1 specific mRNA. RT-PCR was generally performed asdescribed by Fraizer et al., Blood 86:4704–4706, 1995. Total RNA wasextracted from 10⁷ cells according to standard procedures. RNA pelletswere resuspended in 25 μL diethylpyrocarbonate treated water and useddirectly for reverse transcription. The zinc-finger region (exons 7 to10) was amplified by PCR as a 330 bp mouse cDNA. Amplification wasperformed in a thermocycler during one or, when necessary, twosequential rounds of PCR. AmpliTaq DNA Polymerase (Perkin Elmer Cetus,Norwalk, Conn.), 2.5 mM MgCl₂ and 20 pmol of each primer in a totalreaction volume of 50 μl were used. Twenty μL aliquots of the PCRproducts were electrophoresed on 2% agarose gels stained with ethidiumbromide. The gels were photographed with Polaroid film (Polaroid 667,Polaroid Ltd., Hertfordshire, England). Precautions against crosscontamination were taken following the recommendations of Kwok andHiguchi, Nature 339:237–238, 1989. Negative controls included the cDNA-and PCR-reagent mixes with water instead of cDNA in each experiment. Toavoid false negatives, the presence of intact RNA and adequate cDNAgeneration was evaluated for each sample by a control PCR using β-actinprimers. Samples that did not amplify with these primers were excludedfrom analysis.

Primers for amplification of WT1 in mouse cell lines were: P115:1458–1478: 5′CCC AGG CTG CAA TAA GAG ATA 3′ (forward primer; SEQ IDNO:21); and P116: 1767–1787: 5′ ATG TTG TGA TGG CGG ACC AAT 3′ (reverseprimer; SEQ ID NO:22) (see Inoue et al, Blood 88:2267–2278, 1996;Fraizer et al., Blood 86:4704–4706, 1995).

Beta Actin primers used in the control reactions were: 5′ GTG GGG CGCCCC AGG CAC CA 3′ (sense primer; SEQ ID NO:23); and 5′ GTC CTT AAT GTCACG CAC GAT TTC 3′ (antisense primer; SEQ ID NO:24)

Primers for use in amplifying human WT1 include: P117: 954–974: 5′ GGCATC TGA GAC CAG TGA GAA 3′ (SEQ ID NO:25); and P118: 1434–1414: 5′ GAGAGT CAG ACT TGA AAG CAGT 3′ (SEQ ID NO:5). For nested RT-PCR, primersmay be: P119: 1023–1043: 5′ GCT GTC CCA CTT ACA GAT GCA 3′ (SEQ IDNO:26); and P120: 1345–1365: 5′ TCA AAG CGC CAG CTG GAG TTT 3′ (SEQ IDNO:27).

Table XLVIII shows the results of WT1 PCR analysis of mouse tumor celllines. Within Table IV, (+++) indicates a strong WT1 PCR amplificationproduct in the first step RT PCR, (++) indicates a WT1 amplificationproduct that is detectable by first step WT1 RT PCR, (+) indicates aproduct that is detectable only in the second step of WT1 RT PCR, and(−) indicates WT1 PCR negative.

TABLE XLIX Detection of WT1 mRNA in Mouse Tumor Cell Lines Cell Line WT1mRNA K562 (human leukemia; ATCC): Positive control; (Lozzio +++ andLozzio, Blood 45:321–334, 1975) TRAMPC (SV40 transformed prostate, B6);Foster et al., +++ Cancer Res. 57:3325–3330, 1997 BLK-SV40 HD2(SV40–transf. fibroblast, B6; ATCC); ++ Nature 276:510–511, 1978 CTLL(T-cell, B6; ATCC); Gillis, Nature 268:154–156, + 1977) FM (FBL–3subline, leukemia, B6); Glynn and Fefer, + Cancer Res. 28:434–439, 1968BALB 3T3 (ATCC); Aaroston and Todaro, J. Cell. Physiol. + 72:141–148,1968 S49.1 (Lymphoma, T-cell like, B/C; ATCC); Horibata and + Harris,Exp. Cell. Res. 60:61, 1970 BNL CL.2 (embryonic liver, B/C; ATCC);Nature 276: + 510–511, 1978 MethA (sarcoma, B/C); Old et al., Ann. NYAcad. Sci. − 101:80–106, 1962 P3.6.2.8.1 (myeloma, B/C; ATCC); Proc.Natl. Acad. Sci. − USA 66:344, 1970 P2N (leukemia, DBA/2; ATCC); Mellinget al., J. − Immunol. 117:1267–1274, 1976 BCL1 (lymphoma, B/C; ATCC);Slavin and Strober, Nature − 272:624–626, 1977 LSTRA (lymphoma, B/C);Glynn et al., Cancer Res. − 28:434–439, 1968 E10/EL–4 (lymphoma, B6);Glynn et al., Cancer Res. − 28:434–439, 1968

From the foregoing it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

1. A polypeptide consisting of an immunogenic portion of a native WT1,wherein the polypeptide consists of the polypeptide set forth in SEQ IDNO:144.
 2. A polypeptide, wherein the polypeptide consists of 4–9consecutive amino acids of SEQ ID NO:144.
 3. A polypeptide, wherein thepolypeptide consists of 8–9 consecutive amino acids of SEQ ID NO:144. 4.A pharmaceutical composition comprising the polypeptide of claim 1 incombination with a pharmaceutically acceptable carrier or excipient.